Order parameter modeling of fluid dynamics in narrow confinements subjected to hydrophobic interactions

A novel phase-field approach is developed for quantitative modeling of the complex thermophysics over reduced length scales in narrow fluidic confinements, as induced by the surface roughness-hydrophobicity coupling and the consequent hydrodynamic interactions. The method is tested for flows on micro- and nano- corrugated surfaces in narrow confinements, and the agreement with molecular dynamics and lattice Boltzmann simulations is found to be quantitative.     

Mechanical effect of van der waals interactions observed in real time in an ultracold Rydberg gas

We present time-resolved spectroscopic measurements of Rydberg-Rydberg interactions between two Rydberg atoms in an ultracold gas, revealing the pair dynamics induced by long-range van der Waals interactions between the atoms. By detuning the excitation laser, a specific pair distribution is prepared. Penning ionization on a microsecond time scale serves as a probe for the pair dynamics under the influence of the attractive long-range forces. Comparison with a Monte Carlo model not only explains all spectroscopic features but also gives quantitative information about the interaction potentials. The results imply that the interaction-induced ionization rate can be influenced by the excitation laser. Surprisingly, interaction-induced ionization is also observed for Rydberg states with purely repulsive interactions.     

Theoretical study on interaction of cytochrome f and plastocyanin complex by a simple coarse-grained model with molecular crowding effect

ABSTRACT

We present a simple coarse-grained model with the molecular crowding effect in solvent to investigate the structure and dynamics of protein complexes including association and/or dissociation processes and investigate some physical properties such as the structure and the reaction rate from the viewpoint of the hydrophobic intermolecular interactions of protein complex. In the present coarse-grained model, a function depending upon the density of hydrophobic amino acid residues in a binding area of the complex is introduced, and the function involves the molecular crowding effect for the intermolecular interactions of hydrophobic amino acid residues between proteins. We propose a hydrophobic intermolecular potential energy between proteins by using the density-dependent function. The present coarse-grained model is applied to the complex of cytochrome f and plastocyanin by using the Langevin dynamics simulation to investigate some physical properties such as the complex structure, the electron transfer reaction rate constant from plastocyanin to cytochrome f and so on. We find that for proceeding the electron transfer reaction, the distance between metals in their active sites is necessary within about 18 Å. We discuss some typical complex structures formed in the present simulation in relation to the molecular crowding effect on hydrophobic interactions.     

Multiscale models for the growth of avascular tumors

In the past 30 years we have witnessed an extraordinary progress on the research in the molecular biology of cancer, but its medical treatment, widely based on empirically established protocols, still has many limitations. One of the reasons for that is the limited quantitative understanding of the dynamics of tumor growth and drug response in the organism. In this review we shall discuss in general terms the use of mathematical modeling and computer simulations related to cancer growth and its applications to improve tumor therapy. Particular emphasis is devoted to multiscale models which permit integration of the rapidly expanding knowledge concerning the molecular basis of cancer and the complex, nonlinear interactions among tumor cells and their microenvironment that will determine the neoplastic growth at the tissue level.     

Ordered clusters and dynamical states of particles in a vibrated fluid

Fluid-mediated interactions between particles in a vibrating fluid lead to both long range attraction and short range repulsion. The resulting patterns include hexagonally ordered microcrystallites, time-periodic structures, and chaotic fluctuating patterns with complex dynamics. A model based on streaming flow gives a good quantitative account of the attractive part of the interaction.     

Intermolecular and intramolecular contributions to the relaxation process in sorbitol and maltitol

Molecular mobility in sorbitol and maltitol is studied with spectroscopic techniques and molecular dynamics simulations in order to evaluate the relative contributions of the intermolecular and intramolecular interactions involved in the relaxation processes. The results of the molecular dynamics simulations performed on the polyols in the bulk or in vacuum compares well with the results of the analysis of the relaxation diagrams in the framework of the Perez et al. model. They both imply that the difference in the relative contributions of the intermolecular and intramolecular interactions associated with the different chemical architectures of the two polyols must be taken into account. The intermolecular interactions cannot be neglected and they are stronger in sorbitol than in maltitol in relation with the linear structure of this polyol. The intramolecular barrier, higher in the maltitol molecule with a more complex structure, could be at the origin of the higher junction temperature between the α and β relaxation processes.     

How Does van der Waals Confinement Enhance Phonon Transport?

We study the mechanism of van der Waals(vdW)interactions on phonon transport in atomic scale,which would boost developments in heat management and energy conversion.Commonly,the vdW interactions are regarded as a hindrance in phonon transport.Here we propose that the vdW confinement can enhance phonon transport.Through molecular dynamics simulations,it is realized that the vdW confinement is able to make more than two-fold enhancement on thermal conductivity of both polyethylene single chain and graphene nanoribbon.The quantitative analyses of morphology,local vdW potential energy and dynamical properties are carried out to reveal the underlying physical mechanism.It is found that the confined vdW potential barriers reduce the atomic thermal displacement magnitudes,leading to less phonon scattering and facilitating thermal transport.Our study offers a new strategy to modulate the phonon transport.     

CaF2熔化温度的分子动力学模拟

利用壳层模型分子动力学方法,研究了高温高压条件下CaF2的熔化温度,同时计算了温度为300K、压强上升到100GPa时CaF2 的状态方程.研究中考虑了分子动力学模拟的过热熔化,通过晶体的现代熔化理论,对CaF2 的分子动力学模拟熔化温度进行了修正, 获得了高温高压下CaF2的熔化温度.因此,常压下壳层模型分子动力学方法为研究物质熔化提供了一个很好的方法.     

Generalization of interfacial electrohydrodynamics in the presence of hydrophobic interactions in narrow fluidic confinements

We show that the interfacial electromechanics in narrow fluidic confinements exhibits a universal dependence with the intrinsic surface-wettability characteristics, independent of the details of the bulk flow actuating mechanisms. Towards this proposition, we develop a generalized mesoscale model, which is extensively tested for combined electro-osmotic and pressure-driven nanochannel flows. Agreement with the molecular dynamics simulations is found to be quantitative.     

Hadronization from color interactions

A quark coalescence model, based on semi-relativistic molecular dynamics with color interactions among quarks, is presented and applied to pp collisions. A phenomenological potential with two tunable parameters is introduced to describe the color interactions between quarks and antiquarks. The interactions drive the process of hadronization that finally results in different color neutral clusters, which can be identified as hadrons based on some criteria. A Monte Carlo generator PYTHIA is used to generate quarks in the initial state of hadronization, and different values of tunable parameters are used to study the final state distributions and correlations. Baryon-to-meson ratio, transverse momentum spectra, pseudorapidity distributions and forward-backward multiplicity correlations of hadrons produced in the hadronization process, obtained from this model with different parameters, are compared with those from PYTHIA.     

Heating rate effects for the melting transition of Pt-Ag-Au nanoalloys

The classical molecular dynamics simulations in canonical NVT ensemble conditions are used to investigate the melting transition in different heating rates of Pt-Ag-Au ternary nanoalloys. In order to obtain the initial configurations used in the molecular dynamics simulations, optimizing the chemical ordering of Pt₁₃Ag_nAu_42-n (n=0-42) ternary nanoalloys was performed using the Basin-Hopping algorithm which would not allow changes in the icosahedron structure. The Gupta many-body potential was used to model interatomic interactions in both molecular dynamics simulations and optimization simulations. The melting transitions of selected Pt-Ag-Au nanoalloys were explored using caloric curves and Lindemann parameters. There have been two identified types of melting mechanisms, one includes sudden jump behavior in the caloric curve and the other is an isomerization while melting transition. The temperature range in which the isomerization takes place depends on the heating rate value.     

Collective dynamics of interacting molecular motors

The collective dynamics of N interacting processive molecular motors are considered theoretically when an external force is applied to the leading motor. We show, using a discrete lattice model, that the force-velocity curves strongly depend on the effective dynamic interactions between motors and differ significantly from those of a simple approach where the motors equally share the force. Moreover, they become essentially independent of the number of motors if N is large enough (N> or approximately 5 for conventional kinesin). We show that a two-state ratchet model has a very similar behavior to that of the coarse-grained lattice model with effective interactions. The general picture is unaffected by motor attachment and detachment events.     

Formation of argon cluster with proton seeding

ABSTRACT

We employ force-field molecular dynamics simulations to investigate the kinetics of nucleation to new liquid or solid phases in a dense gas of particles, seeded with ions. We use precise atomic pair interactions, with physically correct long-range behaviour, between argon atoms and protons. Time dependence of molecular cluster formation is analysed at different proton concentration, temperature and argon gas density. The modified phase transitions with proton seeding of the argon gas are identified and analysed. The seeding of the gas enhances the formation of nano-size atomic clusters and their aggregation. The strong attraction between protons and bath gas atoms stabilises large nano-clusters and the critical temperature for evaporation. An analytical model is proposed to describe the stability of argon-proton droplets and is compared with the molecular dynamics simulations.     

Controlling density fluctuations in wall-bounded dissipative particle dynamics systems

Dissipative Particle Dynamics (DPD) simulations of wall-bounded flows exhibit density fluctuations that depend strongly on the no-slip boundary condition and increase with the level of coarse graining. We develop an adaptive model for wall-particle interactions that eliminates such oscillations and can target prescribed density profiles. Comparisons are made with ideal no-slip boundary conditions and molecular dynamics simulations. The new model is general and can be used in other coarse-grained particle methods.     

Long-range correction for dipolar fluids at planar interfaces

A slab-based long-range correction for dipolar interactions in molecular dynamics simulation of systems with a planar geometry is presented and applied to simulate vapour–liquid interfaces. The present approach is validated with respect to the saturated liquid density and the surface tension of the Stockmayer fluid and a molecular model for ethylene oxide. The simulation results exhibit no dependence on the cut-off radius for radii down to 1 nm, proving that the long-range correction accurately captures the influence of the dipole moment on the intermolecular interaction energies and forces as well as the virial and the surface tension.     

Aggregation kinetics in a model colloidal suspension

We present molecular dynamics simulations of aggregation kinetics in a colloidal suspension modeled as a highly asymmetric binary mixture. Starting from a configuration with largely uncorrelated colloidal particles the system relaxes by coagulation-fragmentation dynamics to a structured state of low-dimensionality clusters with an exponential size distribution. The results show that short-range repulsive interactions alone can give rise to so-called cluster phases. For the present model and probably other, more common colloids, the observed clusters appear to be equilibrium phase fluctuations induced by the entropic intercolloidal attractions.     

Structural and dynamical aspects of water in contact with a hydrophobic surface

By means of molecular dynamics simulations we study the structure and dynamics of water molecules in contact with a model hydrophobic surface: a planar graphene-like layer. The analysis of the distributions of a local structural index indicates that the water molecules proximal to the graphene layer are considerably more structured than the rest and, thus, than the bulk. This structuring effect is lost in a few angstroms and is basically independent of temperature for a range studied comprising parts of both the normal liquid and supercooled states (240K to 320K). In turn, such structured water molecules present a dynamics that is slower than the bulk, as a consequence of their improved interactions with their first neighbors.     

Influence of hydrodynamic interactions on lane formation in oppositely charged driven colloids

The influence of hydrodynamic interactions on lane formation of oppositely charged driven colloidal suspensions is investigated using Brownian dynamics computer simulations performed on the Rotne-Prager level of the mobility tensor. Two cases are considered, namely sedimentation and electrophoresis. In the latter case the Oseen contribution to the mobility tensor is screened due to the opposite motion of counterions. The simulation results are compared to that resulting from simple Brownian dynamics where hydrodynamic interactions are neglected. For sedimentation, we find that hydrodynamic interactions strongly disfavor laning. In the steady state of lanes, a macroscopic phase separation of lanes is observed. This is in marked contrast to the simple Brownian case where a finite size of lanes was obtained in the steady state. For strong Coulomb interactions between the colloidal particles a lateral square lattice of oppositely driven lanes is stable similar to the simple Brownian dynamics. In an electric field, on the other hand, the behavior is found in qualitative and quantitative accordance with the case of neglected hydrodynamics.     

Chromatin code, local non-equilibrium dynamics, and the emergence of transcription regulatory programs

Chromatin is a, if not the, hallmark of eukaryotic life. Any molecular process entailing genomic DNA or the nucleus by default provokes or depends on chromatin structural dynamics on various space and time scales. Chromatin dynamics are result of changes in the physico-chemical properties of the chromatin constituents themselves or the nuclear environment. Chromatin has been found in the former case to undergo many different covalent enzyme-mediated chemical modifications. Their identification sheds light on the molecular mechanisms and the physico-chemical properties underlying chromatin dynamics, and allows the development of quantitative models for the chromatin fiber. The abundance of the different modifications, their dynamics, and short- as well as long-range correlation phenomena between different modifications also point to a second layer of genomic coding implemented at the level of chromatin. Especially, gene regulatory coding seems to depend on such a second-level code. The information-theoretical properties of chromatin in the context of gene regulatory coding are discussed. A model for the emergence of cellular differentiation from the intricate interplay between genomic and chromatin code is presented and discussed in light of recent experimental insights.