Topic overview

physics.chem-ph

3385 works10757 researchers

Map preview

Start with the graph, then narrow the list

3385works
10757researchers

Next steps

Use the topic as a working map

Open the full map for clusters, then return here to scan ranked papers and people.

Topic graph

See the topic as a live network

Open full explorer

Inspect nearby papers, researchers, institutions and communities without opening a separate graph page.

Building this map preview

BZPEER is loading the nearby papers, people, topics and institutions for this page.

Papers in this area

24 paper(s) to start with

preprint2016arXiv

Stochastic Dynamics of Extended Objects in Driven Systems II: Current Quantization in the Low-Temperature Limit

Driven Langevin processes have appeared in a variety of fields due to the relevance of natural phenomena having both deterministic and stochastic effects. The stochastic currents and fluxes in these systems provide a convenient set of observables to describe their non-equilibrium steady states. Here we consider stochastic motion of a (k - 1)-dimensional object, which sweeps out a k-dimensional trajectory, and gives rise to a higher k-dimensional current. By employing the low-temperature (low-noise) limit, we reduce the problem to a discrete Markov chain model on a CW complex, a topological construction which generalizes the notion of a graph. This reduction allows the mean fluxes and currents of the process to be expressed in terms of solutions to the discrete Supersymmetric Fokker-Planck (SFP) equation. Taking the adiabatic limit, we show that generic driving leads to rational quantization of the generated higher dimensional current. The latter is achieved by implementing the recently developed tools, coined the higher-dimensional Kirchhoff tree and co-tree theorems. This extends the study of motion of extended objects in the continuous setting performed in the prequel to this man

preprint2016arXiv

Wave propagation in spatially modulated tubes

We investigate wave propagation in rotationally symmetric tubes with a periodic spatial modulation of cross section. Using an asymptotic perturbation analysis, the governing quasi two-dimensional reaction-diffusion equation can be reduced into a one-dimensional reaction-diffusion-advection equation. Assuming a weak perturbation by the advection term and using projection method, in a second step, an equation of motion for traveling waves within such tubes can be derived. Both methods predict properly the nonlinear dependence of the propagation velocity on the ratio of the modulation period of the geometry to the intrinsic width of the front, or pulse. As a main feature, we can observe finite intervals of propagation failure of waves induced by the tube's modulation. In addition, using the Fick-Jacobs approach for the highly diffusive limit we show that wave velocities within tubes are governed by an effective diffusion coefficient. Furthermore, we discuss the effects of a single bottleneck on the period of pulse trains within tubes. We observe period changes by integer fractions dependent on the bottleneck width and the period of the entering pulse train.

preprint2016arXiv

Electronic Single Molecule Identification of Carbohydrate Isomers by Recognition Tunneling

Glycans play a central role as mediators in most biological processes, but their structures are complicated by isomerism. Epimers and anomers, regioisomers, and branched sequences contribute to a structural variability that dwarfs those of nucleic acids and proteins, challenging even the most sophisticated analytical tools, such as NMR and mass spectrometry. Here, we introduce an electron tunneling technique that is label-free and can identify carbohydrates at the single-molecule level, offering significant benefits over existing technology. It is capable of analyzing sub-picomole quantities of sample, counting the number of individual molecules in each subset in a population of coexisting isomers, and is quantitative over more than four orders of magnitude of concentration. It resolves epimers not well separated by ion-mobility and can be implemented on a silicon chip. It also provides a readout mechanism for direct single-molecule sequencing of linear oligosaccharides.

preprint2016arXiv

Modified Kedem-Katchalsky equations for osmosis through nano-pore

This work presents a modified Kedem-Katchalsky equations for osmosis through nano-pore. osmotic reflection coefficient of a solute was found to be chiefly affected by the entrance of the pore while filtration reflection coefficient can be affected by both the entrance and the internal structure of the pore. Using an analytical method, we get the quantitative relationship between osmotic reflection coefficient and the molecule size. The model is verified by comparing the theoretical results with the reported experimental data of aquaporin osmosis. Our work is expected to pave the way for a better understanding of osmosis in bio-system and to give us new ideas in designing new membranes with better performance.

preprint2016arXiv

Self-Metalation of Phthalocyanine Molecules with Silver Surface Atoms by Adsorption on Ag(110)

We report that metal-free phthalocyanine (H2Pc) molecules with a central cavity are able to incorporate Ag atoms from an Ag(110) surface thus creating silver-phthalocyanine (AgPc). The reaction was investigated by means of scanning tunneling microscopy (STM) under ultrahigh vacuum, and the metalation of \ce{H2Pc} at the interface was confirmed with X-ray photoelectron spectroscopy. Three different kinds of molecules were found on the surface that are assigned to H2Pc, the corresponding dehydrogenated molecules (Pc) and AgPc. The relative amounts of Pc and AgPc increase with increasing annealing temperature. We suggest that the reaction with Ag atoms from the steps of the surface occurs favorably only for already dehydrogenated molecules; thus, the metalation of H2Pc is likely limited by the heat-induced dehydrogenation. Density functional theory simulations of the reaction path are presented to corroborate this hypothesis.

preprint2016arXiv

High-resolution absorption measurements of NH3 at high temperatures: 2100 - 5500

High-resolution absorption spectra of \NH\ in the region 2100 - 5500 \cm\ at 1027 $^{\circ}$C and atmospheric pressure (1045 $\pm$ 3 mbar) are measured. An \NH\ concentration of 10\% in volume fraction is used in the measurements. Spectra are recorded in a high-temperature gas-flow cell using a Fourier Transform Infrared (FTIR) spectrometer at a nominal resolution of 0.09 \cm. The spectra are analysed by comparison to a variational line list, BYTe, and experimental energy levels determined using the MARVEL procedure. 2308 lines have been assigned to 45 different bands, of which 1755 and 15 have been assigned or observed for the first time in this work.

preprint2016arXiv

Geometric Phase Effects in the Ultracold D + HD $\to$ D + HD and D + HD $\leftrightarrow$ H + D$_2$ Reactions

The results of accurate quantum reactive scattering calculations for the D + HD($v=4$, $j=0$) $\to$ D + HD($v'$, $j'$), D + HD($v=4$, $j=0$) $\to$ H + D$_2$($v'$, $j'$) and H + D$_2$($v=4$, $j=0$) $\to$ D + HD($v'$,$j'$) reactions are presented for collision energies between $1\,μ{\rm K}$ and $100\,{\rm K}$. The ${\it ab\ initio}$ BKMP2 PES for the ground electronic state of H$_3$ is used and all values of total angular momentum between $J=0-4$ are included. The general vector potential approach is used to include the geometric phase. The rotationally resolved, vibrationally resolved, and total reaction rate coefficients are reported as a function of collision energy. Rotationally resolved differential cross sections are also reported as a function of collision energy and scattering angle. Large geometric phase effects appear in the ultracold reaction rate coefficients which result in a significant enhancement or suppression of the rate coefficient (up to $3$ orders of magnitude) relative to calculations which ignore the geometric phase. The results are interpreted using a new quantum interference mechanism which is unique to ultracold collisions. Significan

preprint2016arXiv

Structure and dynamics of H$_2^+$ near the dissociation threshold: a combined experimental and computational investigation

The pulsed-field-ionization zero-kinetic-energy photoelectron spectrum of H$_2$ has been recorded in the vicinity of the dissociative-ionization threshold following three-photon excitation via selected rotational levels of the B $^1Σ_u^+$ ($v=19$) and $\bar{\rm H}$ $^1Σ_g^+$ ($v=11$) intermediate states. The spectra consist of transitions to bound levels of the X$^+$ $^2Σ_g^+$ state of H$_2^+$ with $v^+$ in the range 14-19 and $N^+$ in the range 0-9, of the A$^+$ $^2Σ_u^+$ state with $v^+=0$ and $N^+=0-2$, and of shape resonances corresponding to the X$^+\ (v^+=17,N^+=7)$ and X$^+\ (v^+=18,N^+=4)$ quasibound levels. Calculations of the level structure of H$_2^+$ have been carried out and the influence of adiabatic, nonadiabatic, relativistic and radiative corrections on the positions of these levels, and in the case of the shape resonances also on their widths, has been investigated. Different methods of calculating the widths and profiles of the shape resonances have been tested for comparison with the experimental observations. Slow oscillations of the dissociative-ionization yield have been observed and reflect, in first approximation, the Franck-Condon factors of the $\bar{\tex

preprint2016arXiv

An efficient quantum mechanical method for radical pair recombination reactions

The standard quantum mechanical expressions for the singlet and triplet survival probabilities and product yields of a radical pair recombination reaction involve a trace over the states in a combined electronic and nuclear spin Hilbert space. If this trace is evaluated deterministically, by performing a separate time-dependent wavepacket calculation for each initial state in the Hilbert space, the computational effort scales as $O(Z^2\log Z)$, where $Z$ is the total number of nuclear spin states. Here we show that the trace can also be evaluated stochastically, by exploiting the properties of spin coherent states. This results in a computational effort of $O(MZ\log Z)$, where $M$ is the number of Monte Carlo samples needed for convergence. Example calculations on a strongly-coupled radical pair with $Z>10^6$ show that the singlet yield can be converged to graphical accuracy using just $M=200$ samples, resulting in a speed up by a factor of $>5000$ over a standard deterministic calculation. We expect that this factor will greatly facilitate future quantum mechanical simulations of a wide variety of radical pairs of interest in chemistry and biology.

preprint2016arXiv

Deviations from Born-Oppenheimer mass scaling in spectroscopy and ultracold molecular physics

We investigate Born-Oppenheimer breakdown (BOB) effects (beyond the usual mass scaling) for the electronic ground states of a series of homonuclear and heteronuclear alkali-metal diatoms, together with the Sr$_2$ and Yb$_2$ diatomics. Several widely available electronic structure software packages are used to calculate the leading contributions to the total isotope shift for commonly occurring isotopologs of each species. Computed quantities include diagonal Born-Oppenheimer corrections (mass shifts) and isotopic field shifts. Mass shifts dominate for light nuclei up to and including K, but field shifts contribute significantly for Rb and Sr and are dominant for Yb. We compare the {\em ab initio} mass-shift functions for Li$_2$, LiK and LiRb with spectroscopically derived ground-state BOB functions from the literature. We find good agreement in the values of the functions for LiK and LiRb at their equilibrium geometries, but significant disagreement with the shapes of the functions for all 3 systems. The differences may be due to contributions of nonadiabatic terms to the empirical BOB functions. We present a semiclassical model for the effect of BOB corrections on the binding ener

preprint2016arXiv

Mathematical Formalism of Nonequilibrium Thermodynamics for Nonlinear Chemical Reaction Systems with General Rate Law

This paper studies a mathematical formalism of nonequilibrium thermodynamics for chemical reaction models with $N$ species, $M$ reactions, and general rate law. We establish a mathematical basis for J. W. Gibbs' macroscopic chemical thermodynamics under G. N. Lewis' kinetic law of entire equilibrium (detailed balance in nonlinear chemistry kinetics). In doing so, the equilibrium thermodynamics is then naturally generalized to nonequilibrium settings without detailed balance. The kinetic models are represented by a Markovian jumping process. A generalized macroscopic chemical free energy function and its associated balance equation with nonnegative source and sink are the major discoveries. The proof is based on the large deviation principle of this type of Markov processes. A general fluctuation dissipation theorem for stochastic reaction kinetics is also proved. The mathematical theory illustrates how a novel macroscopic dynamic law can emerges from the mesoscopic kinetics in a multi-scale system.

preprint2015arXiv

Scaling of the dynamics of flexible Lennard-Jones chains. II. Effects of harmonic bonds

The previous paper [Veldhorst et al., J. Chem. Phys. 141, 054904 (2014)] demonstrated that the isomorph theory explains the scaling properties of a liquid of flexible chains consisting of ten Lennard-Jones particles connected by rigid bonds. We here investigate the same model with harmonic bonds. The introduction of harmonic bonds almost completely destroys the correlations in the equilibrium fluctuations of the potential energy and the virial. According to the isomorph theory, if these correlations are strong a system has isomorphs, curves in the phase diagram along which structure, dynamics and the excess entropy are invariant. The Lennard-Jones chain liquid with harmonic bonds does have curves in the phase diagram along which the structure and dynamics are invariant. The excess entropy is not invariant on these curves, which we refer to as "pseudoisomorphs". In particular this means that Rosenfeld's excess-entropy scaling (the dynamics being a function of excess entropy only) does not apply for the Lennard-Jones chain with harmonic bonds.

preprint2016arXiv

Focal overlap gating in velocity map imaging to achieve high signal-to-noise ratio in photo-ion pump-probe experiments

We demonstrate a new technique in velocity map imaging (VMI) that allows spatial gating of the laser focal overlap region in time resolved pump-probe experiments. This significantly enhances signal-to-noise ratio by eliminating background signal arising outside the region of spatial overlap of pump and probe beams. This enhancement is achieved by tilting the laser beams with respect to the surface of the VMI electrodes which creates a gradient in flight time for particles born at different points along the beam. By suitably pulsing our microchannel plate detector, we can select particles born only where the laser beams overlap. This spatial gating in velocity map imaging can benefit nearly all photoion pump-probe VMI experiments especially when extreme-ultraviolet (XUV) light or X-rays are involved which produce large background signals on their own.

preprint2016arXiv

Definitive ideal-gas thermochemical functions of the H$_2$$^{16}$O molecule

$Q_{\rm int}$($T$), of the H$_2$$^{16}$O molecule is reported for temperatures between 0 and 6000 K. Determination of $Q_{\rm int}$($T$) is principally based on the direct summation technique involving all accurate experimental energy levels known for H$_2$$^{16}$O (almost 20~000 rovibrational energies including an almost complete list up to a relative energy of 7500 \cm), augmented with a less accurate but complete list of first-principles computed rovibrational energy levels up to the first dissociation limit, about 41~000 \cm\ (the latter list includes close to one million bound rovibrational energy levels up to $J = 69$, where $J$ is the rotational quantum number). Partition functions are developed for {\it ortho}- and {\it para}-H$_2$$^{16}$O as well as for their equilibrium mixture. Unbound rovibrational states above the first dissociation limit are considered using an approximate model treatment. The effect of the excited electronic states on the thermochemical functions is neglected, as their contribution to the thermochemical functions is negligible even at the highest temperatures considered. Based on the high-accuracy $Q_{\rm int}$($T$) and its first two moments, definit

preprint2016arXiv

Hydrogen bonding in the protic ionic liquid triethylammonium nitrate explored by density functional tight binding simulations

The applicability of the density functional based tight binding (DFTB) method to the description of hydrogen bond dynamics and infrared spectroscopy is addressed for the exemplary protic ionic liquid triethylammonium nitrate. Potential energy curves for proton transfer in gas and liquid phase are shown to be comparable to high level coupled cluster theory in the thermally accessible range of bond lengths. Geometric correlations in the hydrogen bond dynamics are analyzed for a cluster of six ion pairs. Comparing DFTB and regular DFT data lends further support for the reliability of the DFTB method. Therefore, DFTB bulk simulations are performed to quantify the extent of geometric correlations in terms of Pauling's bond order model. Further, infrared (IR) absorption spectra are obtained and analyzed putting emphasis on the signatures of hydrogen bonding in the NH-stretching and far IR hydrogen bond range.

preprint2015arXiv

Explaining why simple liquids are quasi-universal

It has been known for a long time that many simple liquids have surprisingly similar structure as quantified, e.g., by the radial distribution function. A much more recent realization is that the dynamics are also very similar for a number of systems with quite different pair potentials. Systems with such non-trivial similarities are generally referred to as "quasi-universal". From the fact that the exponentially repulsive pair potential has strong virial potential-energy correlations in the low-temperature part of its thermodynamic phase diagram, we here show that a liquid is quasi-universal if its pair potential can be written approximately as a sum of exponential terms with numerically large prefactors. Based on evidence from the literature we moreover conjecture the converse, i.e., that quasi-universality only applies for systems with this property.

preprint2014arXiv

Cooee bitumen II: Stability of linear asphaltene nanoaggregates

Asphaltene and smaller aromatic molecules tend to form linear nanoaggregates in bitumen.Over the years bitumen undergoes chemical aging and during this process, the size of the nanoaggregate increases. This increase is associated with an increase in viscosity and brittleness of the bitumen, eventually leading to road deterioration. This paper focuses on understanding the mechanisms behind nanoaggregate size and stability. We used molecular dynamics simulations to quantify the probability of having a nanoaggregate of a given size in the stationary regime. To model this complicated behavior, we chose first to consider the simple case where only asphaltene molecules are counted in a nanoaggregate. We used a master equation approach and a related statistical mechanics model. The linear asphaltene nanoaggregates behave as a rigid linear chain. The most complicated case where all aromatic molecules are counted in a nanoaggregate is then discussed. The linear aggregates where all aromatic molecules are counted seem to behave as a flexible linear chain.

preprint2016arXiv

Performance of a Nonempirical Density Functional on Molecules and Hydrogen-Bonded Complexes

Recently, Tao and Mo (TM) derived a meta-generalized gradient approximation functional based on a model exchange-correlation hole. In this work, the performance of this functional is assessed on standard test sets, using the 6-311++G(3df,3pd) basis set. These test sets include 223 G3/99 enthalpies of formation, 99 atomization energies, 76 barrier heights, 58 electron affinities, 8 proton affinities, 96 bond lengths, 82 harmonic vibrational frequencies, 10 hydrogen-bonded molecular complexes, and 22 atomic excitation energies. Our calculations show that the TM functional can achieve high accuracy for most properties considered, relative to the LSDA, PBE, and TPSS functionals. In particular, it yields the best accuracy for proton affinities, harmonic vibrational frequencies, hydrogen-bonded dissociation energies and bond lengths, and atomic excitation energies.

preprint2016arXiv

Morphological Aspects of Porous Silicon Prepared by Photoelectrochemical Etching

In this work the effects of coherent radiation (Laser) and incoherent radiation (Halogen lamp) during the electrochemical etching process on the structural characteristics of n-type PSi samples were investigated. The porosity values were measured by depending on the microstructure analyses and Gravimetric measurements. Surface morphology, layer thickness, pore diameter, pore shape, wall thickness and etching rate were studied by depending on Scanning electron-microscopic (SEM) images

preprint2016arXiv

Coupling sample paths to the partial thermodynamic limit in stochastic chemical reaction networks

Many biochemical systems appearing in applications have a multiscale structure so that they converge to piecewise deterministic Markov processes in a thermodynamic limit. The statistics of the piecewise deterministic process can be obtained much more efficiently than those of the exact process. We explore the possibility of coupling sample paths of the exact model to the piecewise deterministic process in order to reduce the variance of their difference. We then apply this coupling to reduce the computational complexity of a Monte Carlo estimator. In addition to rigorous results concerning the asymptotic computational complexity of the Monte Carlo estimator, numerical simulations are performed on some simple biological models confirming that computational gains are made.

preprint2016arXiv

Stochastic Dynamics of Extended Objects in Driven Systems: I. Higher-Dimensional Currents in the Continuous Setting

The probability distributions, as well as the mean values of stochastic currents and fluxes, associated with a driven Langevin process, provide a good and topologically protected measure of how far a stochastic system is driven out of equilibrium. By viewing a Langevin process on a compact oriented manifold of arbitrary dimension m as a theory of a random vector field associated with the environment, we are able to consider stochastic motion of higher-dimensional objects, which allow new observables, called higher-dimensional currents, to be introduced. These higher dimensional currents arise by counting intersections of a k-dimensional trajectory, produced by a evolving (k-1)-dimensional cycle, with a reference cross section, represented by a cycle of complimentary dimension (m - k). We further express the mean fluxes in terms of the solutions of the Supersymmetric Fokker-Planck (SFP), thus generalizing the corresponding well-known expressions for the conventional currents.

preprint2016arXiv

Theoretical evaluation of electrochemical cell architectures using cation intercalation electrodes for desalination

Water scarcity is a dilemma facing much of the global population. Cation intercalation desalination (CID) cells, which use intercalation host compounds (IHCs) in combination with ion-exchange membranes (IEMs), could aid in addressing this challenge by treating saline water sources. Originally, the performance of such cells was predicted utilizing continuous flow of saline water through porous IHC electrodes. Here, we use two-dimensional porous-electrode theory with concentrated solution transport to evaluate the performance of various cell architectures where flow occurs through open flow channels (OFCs) when two IHC electrodes comprised of nickel hexacyanoferrate (NiHCF) are used to store Na+ ions. We show that, when two OFCs are used, cation exchange membranes (CEMs) are adjoined at flow-channel/electrode interfaces, and an anion exchange membrane (AEM) is arranged between flow channels, salt removal increases relative to the original design with flow-through (FT) electrodes. The IEM stacking sequence within such a membrane flow-by (MFB) cell is the fundamental repeat unit for electrodialysis (ED) stacks using many IEMs (CEM/AEM/.../CEM/AEM/CEM) with many diluate streams. Accordi

preprint2016arXiv

Photoexcitation Circular Dichroism in Chiral Molecules

Chirality is ubiquitous in nature and fundamental in science, from particle physics to metamaterials.The most established technique of chiral discrimination - photoabsorption circular dichroism - relies on the magnetic properties of a chiral medium and yields an extremely weak chiral response. We propose and demonstrate a new, orders of magnitude more sensitive type of circular dichroism in neutral molecules: photoexitation circular dichroism. It does not rely on weak magnetic effects, but takes advantage of the coherent helical motion of bound electrons excited by ultrashort circularly polarized light. It results in an ultrafast chiral response and the efficient excitation of a macroscopic chiral density in an initially isotropic ensemble of randomly oriented chiral molecules. We probe this excitation without the aid of further chiral interactions using linearly polarized laser pulses. Our time-resolved study of vibronic chiral dynamics opens a way to the efficient initiation, control and monitoring of chiral chemical change in neutral molecules at the level of electrons.

preprint2016arXiv

Dirac Nodal Lines and Tilted Semi-Dirac Cones Coexisting in a Striped Boron Sheet

The enchanting Dirac fermions in graphene stimulated us to seek for other two-dimensional (2D) Dirac materials, and boron monolayers may be a good candidate. So far, a number of monolayer boron sheets have been theoretically predicted, and three have been experimentally prepared. However, none of them possesses Dirac electrons. Herein, by means of density functional theory (DFT) computations, we identified a new boron monolayer, namely hr-sB, with two types of Dirac fermions coexisting in the sheet: one type is related to Dirac nodal lines traversing Brillouin zone (BZ) with velocities approaching 106 m/s, the other is related to tilted semi-Dirac cones with strong anisotropy. This newly predicted boron monolayer consists of hexagon and rhombus stripes. With an exceptional stability comparable to the experimentally achieved boron sheets, it is rather optimistic to grow hr-sB on some suitable substrates such as the Ag (111) surface. The unique electronic properties induced by special bond characteristics also imply that this boron monolayer may be a good superconductor.

People in this topic

12 visible researcher(s)