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Published work

25 published item(s)

preprint2026arXiv

Three-Stage Learning Unlocks Strong Performance in Simple Models for Long-Term Time Series Forecasting

Recent studies on long-term time series forecasting have shown that simple linear models and MLP-based predictors can achieve strong performance without increasingly complex architectures. However, many competitive baselines still rely on structural priors such as frequency-domain modeling, explicit decomposition, multi-scale mixing, or sophisticated cross-variable interaction modules, while paying less attention to how simple temporal mappings should be trained and organized. In this paper, we propose STAIR, short for Stagewise Temporal Adaptation via Individualization and Residual Learning, a training paradigm for long-term time series forecasting that aims to unlock the capacity of simple temporal mapping models without introducing complex architectural modules. STAIR decomposes forecasting ability into three progressive stages: it first learns common temporal dynamics across variables through a shared temporal mapping, then adapts the shared model to each variable via channel-wise fine-tuning to capture variable-specific patterns, and finally complements the backbone with cross-variable information through residual learning. We further introduce Shared-to-Individual Fine-tuning and alpha-RevIN to mitigate the limitations of strict channel independence and the overly strong normalization prior induced by standard RevIN. This design gradually increases modeling flexibility while keeping the core temporal predictor as a shallow MLP in the main experiments, with linear variants analyzed separately. Experiments on nine long-term forecasting benchmarks show that STAIR matches or outperforms recent strong baselines while preserving a simple temporal backbone, providing a concise and effective modeling perspective for long-term time series forecasting.

preprint2022arXiv

On the $L_p$ Brunn-Minkowski theory and the $L_p$ Minkowski problem for $C$-coconvex sets

Let $C$ be a pointed closed convex cone in $\mathbb{R}^n$ with vertex at the origin $o$ and having nonempty interior. The set $A\subset C$ is $C$-coconvex if the volume of $A$ is finite and $A^{\bullet}=C\setminus A$ is a closed convex set. For $0<p<1$, the $p$-co-sum of $C$-coconvex sets is introduced, and the corresponding $L_p$ Brunn-Minkowski inequality for $C$-coconvex sets is established. We also define the $L_p$ surface area measures, for $0\neq p\in \mathbb{R}$, of certain $C$-coconvex sets, which are critical in deriving a variational formula of the volume of the Wulff shape associated with a family of functions obtained from the $p$-co-sum. This motivates the $L_p$ Minkowski problem aiming to characterize the $L_p$ surface area measures of $C$-coconvex sets. The existence of solutions to the $L_p$ Minkowski problem for all $0\neq p\in \mathbb{R}$ is established. The $L_p$ Minkowski inequality for $0<p<1$ is proved and is used to obtain the uniqueness of the solutions to the $L_p$ Minkowski problem for $0<p<1$. For $p=0$, we introduce $(1-τ)\diamond A_1\oplus_0τ\diamond A_2$, the log-co-sum of two $C$-coconvex sets $A_{1}$ and $A_{2}$ with respect to $τ\in(0, 1)$, and prove the log-Brunn-Minkowski inequality of $C$-coconvex sets. The log-Minkowski inequality is also obtained and is applied to prove the uniqueness of the solutions to the log-Minkowski problem that characterizes the cone-volume measures of $C$-coconvex sets. Our result solves an open problem raised by Schneider in [Schneider, Adv. Math., 332 (2018), pp. 199-219].

preprint2022arXiv

SerialTrack: ScalE and Rotation Invariant Augmented Lagrangian Particle Tracking

We present a new particle tracking algorithm to accurately resolve large deformation and rotational motion fields, which takes advantage of both local and global particle tracking algorithms. We call this method the ScalE and Rotation Invariant Augmented Lagrangian Particle Tracking (SerialTrack). This method builds an iterative scale and rotation invariant topology-based feature for each particle within a multi-scale tracking algorithm. The global kinematic compatibility condition is applied as a global augmented Lagrangian constraint to enhance the tracking accuracy. An open source software package implementing this numerical approach to track both 2D and 3D, incremental and cumulative deformation fields is provided.

preprint2022arXiv

Site-resolved observables in the doped spin-imbalanced triangular Hubbard model

The suppression of antiferromagnetic ordering in geometrically frustrated Hubbard models leads to a variety of exotic quantum phases including quantum spin liquids and chiral states. Here, we focus on the Hubbard model on one of the simplest frustrated lattice geometries, a triangular lattice. Motivated by the recent realization of ultracold fermionic atoms in triangular optical lattices, we study the properties of the triangular-lattice Hubbard model through a Numerical Linked-Cluster Expansion algorithm. We investigate the Mott insulator transition finding a critical interaction $U_c/t = 7.0(2)$ and use spatial two- and three-point correlation functions to explore doped and imbalanced systems. Our results demonstrate that many interesting features occur at temperatures previously obtained for ultracold fermions in optical lattices and are accessible by upcoming experiments. Our calculations will be helpful for thermometry in ultracold atom quantum simulators and can guide experimental searches for exotic quantum phases in atomic triangular Hubbard quantum simulators.

preprint2021arXiv

Model Synthesis for Communication Traces of System-on-Chip Designs

Concise and abstract models of system-level behaviors are invaluable in design analysis, testing, and validation. In this paper, we consider the problem of inferring models from communication traces of system-on-chip~(SoC) designs. The traces capture communications among different blocks of a SoC design in terms of messages exchanged. The extracted models characterize the system-level communication protocols governing how blocks exchange messages, and coordinate with each other to realize various system functions. In this paper, the above problem is formulated as a constraint satisfaction problem, which is then fed to a SMT solver. The solutions returned by the SMT solver are used to extract the models that accept the input traces. In the experiments, we demonstrate the proposed approach with traces collected from a transaction-level simulation model of a multicore SoC design and traces of a more detailed multicore SoC design developed in GEM5 environment.

preprint2021arXiv

Predicting Complex Non-spherical Instability Shapes of Inertial Cavitation Bubbles in Viscoelastic Soft Matter

Inertial cavitation in soft matter is an important phenomenon featured in a wide array of biological and engineering processes. Recent advances in experimental, theoretical, and numerical techniques have provided access into a world full of nonlinear physics, yet most of our quantitative understanding to date has been centered on a spherically symmetric description of the cavitation process. However, cavitation bubble growth and collapse rarely occur in a perfectly symmetrical fashion, particularly in soft materials. Predicting the onset of dynamically arising, non-spherical instabilities has remained a significant, unresolved challenge in part due to the additional constitutive complexities introduced by the surrounding nonlinear viscoelastic solid. Here, we provide a new theoretical model capable of accurately predicting the onset of non-spherical instability shapes of a bubble in a soft material by explicitly accounting for all pertinent nonlinear interactions between the fluid-like cavitation bubble and the solid-like surroundings. Comparison against high-resolution experimental images from laser-induced cavitation events in a polyacrylamide (PA) hydrogel show excellent agreement. Interestingly, and consistent with experimental findings, our model predicts the emergence of various dynamic instability shapes for hoop stretch ratios greater than one in contrast to most quasi-static investigations. Our new theoretical framework not only provides unprecedented insight into the cavitation dynamics in a soft solid, but it also provides a quantitative means of interpreting bubble dynamics relevant to a wide array of engineering and medical applications as well as natural phenomena.

preprint2020arXiv

A Digital Twin for Reconfigurable Intelligent Surface Assisted Wireless Communication

Reconfigurable Intelligent Surface (RIS) has emerged as one of the key technologies for 6G in recent years, which comprise a large number of low-cost passive elements that can smartly interact with the impinging electromagnetic waves for performance enhancement. However, optimally configuring massive number of RIS elements remains a challenge. In this paper, we present a novel digital-twin framework for RIS-assisted wireless networks which we name it Environment-Twin (Env-Twin). The goal of the Env-Twin framework is to enable automation of optimal control at various granularities. In this paper, we present one example of the Env-Twin models to learn the mapping function between the RIS configuration with measured attributes for the receiver location, and the corresponding achievable rate in an RIS-assisted wireless network without involving explicit channel estimation or beam training overhead. Once learned, our Env-Twin model can be used to predict optimal RIS configuration for any new receiver locations in the same wireless network. We leveraged deep learning (DL) techniques to build our model and studied its performance and robustness. Simulation results demonstrate that the proposed Env-Twin model can recommend near-optimal RIS configurations for test receiver locations which achieved close to an upper bound performance that assumes perfect channel knowledge. Our Env-Twin model was trained using less than 2% of the total receiver locations. This promising result represents great potential of the proposed Env-Twin framework for developing a practical RIS solution where the panel can automatically configure itself without requesting channel state information (CSI) from the wireless network infrastructure.

preprint2020arXiv

A Post-Silicon Trace Analysis Approach for System-on-Chip Protocol Debug

Reconstructing system-level behavior from silicon traces is a critical problem in post-silicon validation of System-on-Chip designs. Current industrial practice in this area is primarily manual, depending on collaborative insights of the architects, designers, and validators. This paper presents a trace analysis approach that exploits architectural models of the system-level protocols to reconstruct design behavior from partially observed silicon traces in the presence of ambiguous and noisy data. The output of the approach is a set of all potential interpretations of a system's internal executions abstracted to the system-level protocols. To support the trace analysis approach, a companion trace signal selection framework guided by system-level protocols is also presented, and its impacts on the complexity and accuracy of the analysis approach are discussed. That approach and the framework have been evaluated on a multi-core system-on-chip prototype that implements a set of common industrial system-level protocols.

preprint2020arXiv

Characterizing viscoelastic materials via ensemble-based data assimilation of bubble collapse observations

Viscoelastic material properties at high strain rates are needed to model many biological and medical systems. Bubble cavitation can induce such strain rates, and the resulting bubble dynamics are sensitive to the material properties. Thus, in principle, these properties can be inferred via measurements of the bubble dynamics. Estrada et al. (2018) demonstrated such bubble-dynamic high-strain-rate rheometry by using least-squares shooting to minimize the difference between simulated and experimental bubble radius histories. We generalize their technique to account for additional uncertainties in the model, initial conditions, and material properties needed to uniquely simulate the bubble dynamics. Ensemble-based data assimilation minimizes the computational expense associated with the bubble cavitation model. We test an ensemble Kalman filter (EnKF), an iterative ensemble Kalman smoother (IEnKS), and a hybrid ensemble-based 4D--Var method (En4D--Var) on synthetic data, assessing their estimations of the viscosity and shear modulus of a Kelvin--Voigt material. Results show that En4D--Var and IEnKS provide better moduli estimates than EnKF. Applying these methods to the experimental data of Estrada et al. (2018) yields similar material property estimates to those they obtained, but provides additional information about uncertainties. In particular, the En4D--Var yields lower viscosity estimates for some experiments, and the dynamic estimators reveal a potential mechanism that is unaccounted for in the model, whereby the viscosity is reduced in some cases due to material damage occurring at bubble collapse.

preprint2020arXiv

Mining Message Flows from System-on-Chip Execution Traces

Comprehensive and well-defined specifications are necessary to perform rigorous and thorough validation of system-on-chip (SoC) designs. Message flows specify how components of an SoC design communicate and coordinate with each other to realize various system functions. Message flow specifications are essential for efficient system-level validation and debug for SoC designs. However, in practice such specifications are usually not available, often ambiguous, incomplete, or even contain errors. This paper addresses that problem by proposing a specification mining framework, FlowMiner, that automatically extracts message flows from SoC execution traces, which, unlike software traces, show a high degree of concurrency. A set of inference rules and optimization techniques are presented to improve mining performance and reduce mining complexity. Evaluation of this framework in several experiments shows promising results.

preprint2020arXiv

Mining Message Flows using Recurrent Neural Networks for System-on-Chip Designs

Comprehensive specifications are essential for various activities across the entire validation continuum for system-on-chip (SoC) designs. However, specifications are often ambiguous, incomplete, or even contain inconsistencies or errors. This paper addresses this problem by developing a specification mining approach that automatically extracts sequential patterns from SoC transaction-level traces such that the mined patterns collectively characterize system-level specifications for SoC designs. This approach exploits long short-term memory (LSTM) networks trained with the collected SoC execution traces to capture sequential dependencies among various communication events. Then, a novel algorithm is developed to efficiently extract sequential patterns on system-level communications from the trained LSTM models. Several trace processing techniques are also proposed to enhance the mining performance. We evaluate the proposed approach on simulation traces of a non-trivial multi-core SoC prototype. Initial results show that the proposed approach is capable of extracting various patterns on system-level specifications from the highly concurrent SoC execution traces.

preprint2020arXiv

Single upper limb pose estimation method based on improved stacked hourglass network

At present, most high-accuracy single-person pose estimation methods have high computational complexity and insufficient real-time performance due to the complex structure of the network model. However, a single-person pose estimation method with high real-time performance also needs to improve its accuracy due to the simple structure of the network model. It is currently difficult to achieve both high accuracy and real-time performance in single-person pose estimation. For use in human-machine cooperative operations, this paper proposes a single-person upper limb pose estimation method based on an end-to-end approach for accurate and real-time limb pose estimation. Using the stacked hourglass network model, a single-person upper limb skeleton key point detection model was designed.Deconvolution was employed to replace the up-sampling operation of the hourglass module in the original model, solving the problem of rough feature maps. Integral regression was used to calculate the position coordinates of key points of the skeleton, reducing quantization errors and calculations. Experiments showed that the developed single-person upper limb skeleton key point detection model achieves high accuracy and that the pose estimation method based on the end-to-end approach provides high accuracy and real-time performance.

preprint2016arXiv

SYSTRAN's Pure Neural Machine Translation Systems

Since the first online demonstration of Neural Machine Translation (NMT) by LISA, NMT development has recently moved from laboratory to production systems as demonstrated by several entities announcing roll-out of NMT engines to replace their existing technologies. NMT systems have a large number of training configurations and the training process of such systems is usually very long, often a few weeks, so role of experimentation is critical and important to share. In this work, we present our approach to production-ready systems simultaneously with release of online demonstrators covering a large variety of languages (12 languages, for 32 language pairs). We explore different practical choices: an efficient and evolutive open-source framework; data preparation; network architecture; additional implemented features; tuning for production; etc. We discuss about evaluation methodology, present our first findings and we finally outline further work. Our ultimate goal is to share our expertise to build competitive production systems for "generic" translation. We aim at contributing to set up a collaborative framework to speed-up adoption of the technology, foster further research efforts and enable the delivery and adoption to/by industry of use-case specific engines integrated in real production workflows. Mastering of the technology would allow us to build translation engines suited for particular needs, outperforming current simplest/uniform systems.

preprint2014arXiv

Modeling Epidermis Homeostasis and Psoriasis Pathogenesis

We present a computational model to study the spatiotemporal dynamics of the epidermis homeostasis under normal and pathological conditions. The model consists of a population kinetics model of the central transition pathway of keratinocyte proliferation, differentiation and loss and an agent-based model that propagates cell movements and generates the stratified epidermis. The model recapitulates observed homeostatic cell density distribution, the epidermal turnover time and the multilayered tissue structure. We extend the model to study the onset, recurrence and phototherapy-induced remission of psoriasis. The model considers the psoriasis as a parallel homeostasis of normal and psoriatic keratinocytes originated from a shared stem-cell niche environment and predicts two homeostatic modes of the psoriasis: a disease mode and a quiescent mode. Interconversion between the two modes can be controlled by interactions between psoriatic stem cells and the immune system and by the normal and psoriatic stem cells competing for growth niches. The prediction of a quiescent state potentially explains the efficacy of the multi-episode UVB irradiation therapy and recurrence of psoriasis plaques, which can further guide designs of therapeutics that specifically target the immune system and/or the keratinocytes.

preprint2014arXiv

Production of trilobite Rydberg molecule dimers with thousand-Debye permanent electric dipole moments

We observe that when an ultracold ground state cesium (Cs) atom becomes bound within the electronic cloud of an extended Cs electronic orbit, ultralong-range molecules with giant (kilo-Debye) permanent electric dipole moments form. Large molecular permanent electric dipole moments are challenging to experimentally realize. Meeting this challenge has garnered significant interest because permanent electric dipole moments are important for understanding symmetry breaking in molecular physics, control of chemical reactions and realization of strongly correlated many-body quantum systems. These new hybrid class of `trilobite' molecules are predominated with degenerate Rydberg manifolds, making them difficult to produce with conventional optical association. Their behavior is quantitatively reproduced with detailed coupled-channel calculations.

preprint2013arXiv

Chemical sensing by cell-surface chemoreceptor arrays: the roles of receptor cooperativity and adaptation

Most sensory cells use cross-membrane chemoreceptors to detect chemical signals in the environment. The biochemical properties and spatial organization of chemoreceptors play important roles in achieving and maintaining sensitivity and accuracy of chemical sensing. Here we investigate the effects of receptor cooperativity and adaptation on the limits of gradient sensing. We study a single cell with aggregated chemoreceptor arrays on the cell surface and derive general formula to the limits for gradient sensing from the uncertainty of instantaneous receptor activity. In comparison to independent receptors, we find that cooperativity by non-adaptative receptors could significantly lower the sensing limit in a chemical concentration range determined by the biochemical properties of ligand-receptor binding and ligand-induced receptor activity. Cooperativity by adaptative receptors are beneficial to gradient sensing within a broad range of background concentrations. Our results also show that isotropic receptor aggregate layout on the cell surface represents an optimal configuration to gradient sensing.

preprint2013arXiv

The Myogenic Response in Isolated Rat Cerebrovascular Arteries: Smooth Muscle Cell Model

Previous models of the cerebrovascular smooth muscle cell have not addressed the interaction between the electrical, chemical and mechanical components of cell function during the development of active tension. These models are primarily electrical, biochemical or mechanical in their orientation, and do not permit a full exploration of how the smooth muscle responds to electrical or mechanical forcing. To address this issue, we have developed a new model that consists of two major components: electrochemical and chemomechanical subsystems of the cell. Included in the electrochemical model are models of the electrophysiological behavior of the cell membrane, fluid compartments, Ca2+ release and uptake by the sarcoplasmic reticulum, and cytosolic Ca2+ buffering, particularly by calmodulin. With this subsystem model, we can study the mechanics of the production of intracellular Ca2+ transient in response to membrane voltage clamp pulses. The chemomechanical model includes models of: (a) the chemical kinetics of myosin phosphorylation, and the formation of phosphorylated myosin cross-bridges with actin, as well as, attached latch-type cross-bridges; and (b) a model of force generation and mechanical coupling to the contractile filaments and their attachments to protein structures and the skeletal framework of the cell. The two subsystem models are tested independently and compared with data. Likewise, the complete (combined) cell model responses to voltage pulse stimulation under isometric and isotonic conditions are calculated and compared with measured single cell length-force and force-velocity data obtained from literature. This integrated cell model provides biophysically-based explanations of electrical, chemical and mechanical phenomena in cerebrovascular smooth muscle, and has considerable utility as an adjunct to laboratory research and experimental design.

preprint2012arXiv

Origins of concentration dependence of waiting times for single-molecule fluorescence binding

Binary fluorescence time series obtained from single-molecule imaging experiments can be used to infer protein binding kinetics, in particular, association and dissociation rate constants from waiting time statistics of fluorescence intensity changes. In many cases, rate constants inferred from fluorescence time series exhibit nonintuitive dependence on ligand concentration. Here we examine several possible mechanistic and technical origins that may induce ligand dependence of rate constants. Using aggregated Markov models, we show under the condition of detailed balance that non-fluorescent bindings and missed events due to transient interactions, instead of conformation fluctuations, may underly the dependence of waiting times and thus apparent rate constants on ligand concentrations. In general, waiting times are rational functions of ligand concentration. The shape of concentration dependence is qualitatively affected by the number of binding sites in the single molecule and is quantitatively tuned by model parameters. We also show that ligand dependence can be caused by non-equilibrium conditions which result in violations of detailed balance and require an energy source. As to a different but significant mechanism, we examine the effect of ambient buffers that can substantially reduce the effective concentration of ligands that interact with the single molecules. To demonstrate the effects by these mechanisms, we applied our results to analyze the concentration dependence in a single-molecule experiment EGFR binding to fluorophore-labeled adaptor protein Grb2 by Morimatsu et al. (PNAS,104:18013,2007).

preprint2011arXiv

Energy efficient prediction clustering algorithm for multilevel heterogeneous wireless sensor networks

In designing wireless sensor networks, it is important to reduce energy dissipation and prolong network lifetime. In this paper, a new model with energy and monitored objects heterogeneity is proposed for heterogeneous wireless sensor networks. We put forward an energy-efficient prediction clustering algorithm, which is adaptive to the heterogeneous model. This algorithm enables the nodes to select the cluster head according to factors such as energy and communication cost, thus the nodes with higher residual energy have higher probability to become a cluster head than those with lower residual energy, so that the network energy can be dissipated uniformly. In order to reduce energy consumption when broadcasting in clustering phase and prolong network lifetime, an energy consumption prediction model is established for regular data acquisition nodes. Simulation results show that compared with current clustering algorithms, this algorithm can achieve longer sensor network lifetime, higher energy efficiency and superior network monitoring quality.

preprint2011arXiv

Monte Carlo Algorithm for Simulating Reversible Aggregation of Multisite Particles

We present an efficient and exact Monte Carlo algorithm to simulate reversible aggregation of particles with dedicated binding sites. This method introduces a novel data structure of dynamic bond tree to record clusters and sequences of bond formations. The algorithm achieves a constant time cost for processing cluster association and a cost between $\mathcal{O}(\log M)$ and $\mathcal{O}(M)$ for processing bond dissociation in clusters with $M$ bonds. The algorithm is statistically exact and can reproduce results obtained by the standard method. We applied the method to simulate a trivalent ligand and a bivalent receptor clustering system and obtained an average scaling of $\mathcal{O}(M^{0.45})$ for processing bond dissociation in acyclic aggregation, compared to a linear scaling with the cluster size in standard methods. The algorithm also demands substantially less memory than the conventional method.

preprint2011arXiv

Scaffold-mediated Nucleation of Protein Signaling Complexes: Elementary Principles

Proteins with multiple binding sites play important roles in cell signaling systems by nucleating protein complexes in which, for example, enzymes and substrates are co-localized. Proteins that specialize in this function are called by a variety names, including adapter, linker and scaffold. Scaffold-mediated nucleation of protein complexes can be either constitutive or induced. Induced nucleation is commonly mediated by a docking site on a scaffold that is activated by phosphorylation. Here, by considering minimalist mathematical models, which recapitulate scaffold effects seen in more mechanistically detailed models, we obtain analytical and numerical results that provide insights into scaffold function. These results elucidate how recruitment of a pair of ligands to a scaffold depends on the concentrations of the ligands, on the binding constants for ligand-scaffold interactions, on binding cooperativity, and on the milieu of the scaffold, as ligand recruitment is affected by competitive ligands and decoy receptors. For the case of a bivalent scaffold, we obtain an expression for the unique scaffold concentration that maximally recruits a pair of monovalent ligands. Through simulations, we demonstrate that a bivalent scaffold can nucleate distinct sets of ligands to equivalent extents when the scaffold is present at different concentrations. Thus, the function of a scaffold can potentially change qualitatively with a change in copy number. We also demonstrate how a scaffold can change the catalytic efficiency of an enzyme and the sensitivity of the rate of reaction to substrate concentration. The results presented here should be useful for understanding scaffold function and for engineering scaffolds to have desired properties.

preprint2010arXiv

A Non-Cooperative Method for Path Loss Estimation in Femtocell Networks

A macrocell superposed by indoor deployed femtocells forms a geography-overlapped and spectrum-shared two tier network, which can efficiently improve coverage and enhance system capacity. It is important for reducing inter-tier co-channel interference that any femtocell user (FU) can select suitable access channel according to the path losses between itself and the macrocell users (MUs). Path loss should be estimated non-cooperatively since information exchange is difficult between macrocell and femtocells. In this paper, a novel method is proposed for FU to estimate the path loss between itself and any MU independently. According to the adaptive modulation and coding (AMC) mode information broadcasted by the macrocell base station (BS), FU first estimates the path loss between BS and a MU by using Maximum a Posteriori (MAP) method. The probability distribution function (PDF) and statistics of the transmission power of the MU is then derived. According to the sequence of received powers from the MU, FU estimates the path loss between itself and the MU by using minimum mean square error (MMSE) method. Simulation results show that the proposed method can efficiently estimate the path loss between any FU and any MU in all kinds of conditions.

preprint2010arXiv

Rejection-free kinetic Monte Carlo simulation of multivalent biomolecular interactions

The system-level dynamics of multivalent biomolecular interactions can be simulated using a rule-based kinetic Monte Carlo method in which a rejection sampling strategy is used to generate reaction events. This method becomes inefficient when simulating aggregation processes with large biomolecular complexes. Here, we present a rejection-free method for determining the kinetics of multivalent biomolecular interactions, and we apply the method to simulate simple models for ligand-receptor interactions. Simulation results show that performance of the rejection-free method is equal to or better than that of the rejection method over wide parameter ranges, and the rejection-free method is more efficient for simulating systems in which aggregation is extensive. The rejection-free method reported here should be useful for simulating a variety of systems in which multisite molecular interactions yield large molecular aggregates.

preprint2010arXiv

Rule-based Modeling and Simulation of Biochemical Systems with Molecular Finite Automata

We propose a theoretical formalism, molecular finite automata (MFA), to describe individual proteins as rule-based computing machines. The MFA formalism provides a framework for modeling individual protein behaviors and systems-level dynamics via construction of programmable and executable machines. Models specified within this formalism explicitly represent the context-sensitive dynamics of individual proteins driven by external inputs and represent protein-protein interactions as synchronized machine reconfigurations. Both deterministic and stochastic simulations can be applied to quantitatively compute the dynamics of MFA models. We apply the MFA formalism to model and simulate a simple example of a signal transduction system that involves a MAP kinase cascade and a scaffold protein.

preprint2008arXiv

Kinetic Monte Carlo Method for Rule-based Modeling of Biochemical Networks

We present a kinetic Monte Carlo method for simulating chemical transformations specified by reaction rules, which can be viewed as generators of chemical reactions, or equivalently, definitions of reaction classes. A rule identifies the molecular components involved in a transformation, how these components change, conditions that affect whether a transformation occurs, and a rate law. The computational cost of the method, unlike conventional simulation approaches, is independent of the number of possible reactions, which need not be specified in advance or explicitly generated in a simulation. To demonstrate the method, we apply it to study the kinetics of multivalent ligand-receptor interactions. We expect the method will be useful for studying cellular signaling systems and other physical systems involving aggregation phenomena.