Related papers: Modeling single-molecule stretching experiments us…
Heterogeneity in gene expression across isogenic cell populations can give rise to phenotypic diversity, even when cells are in homogenous environments. This diversity arises from the discrete, stochastic nature of biochemical reactions,…
We formulate theoretical modeling approaches and develop practical computational simulation methods for investigating the non-equilibrium statistical mechanics of fluid interfaces with passive and active immersed particles. Our approaches…
Molecular dynamics refers to the computer simulation of a material at the atomic level. An open problem in numerical analysis is to explain the apparent reliability of molecular dynamics simulations. The difficulty is that individual…
The plasticity of amorphous solids undergoing shear is characterized by quasi-localized rearrangements of particles. While many models of plasticity exist, the precise relationship between plastic dynamics and the structure of a particle's…
One-dimensional model for study of sub--femtosecond experiment with metal surface is put forward. The important features of the system, such as the pseudopotential for electron motion in the metal bulk, abrupt decrease of the normal to the…
The effect of finite temperature $T$ and finite strain rate $\dot\gamma$ on the statistical physics of plastic deformations in amorphous solids made of $N$ particles is investigated. We recognize three regimes of temperature where the…
By quantitative studies of statistics of polymer stretching in a random flow and of a flow field we demonstrate that the stretching of polymer molecules in a 3D random flow occurs rather sharply via the coil-stretch transition at the value…
A binary mixture of particles interacting with spherically-symmetric potentials leading to microsegregation is studied by theory and molecular dynamics (MD) simulations. We consider spherical particles with equal diameters and volume…
The non-equilibrium statistical mechanics and kinetic theory for a model of a confined quasi-two-dimensional gas of inelastic hard spheres is presented. The dynamics of the particles includes an effective mechanism to transfer the energy…
Stochastic thermodynamics is formulated under the assumption of perfect knowledge of all thermodynamic parameters. However, in any real-world experiment, there is non-zero uncertainty about the precise value of temperatures, chemical…
We use mesoscopic non-equilibrium thermodynamics theory to describe RNA unfolding under tension. The theory introduces reaction coordinates, characterizing a continuum of states for each bond in the molecule. The unfolding considered is so…
Using a non-perturbative classical model, we numerically investigate the dynamics of mobile particles interacting with an infinite chain of harmonic oscillators, an abstraction of ionic conduction through solid-state materials. We show that…
Molecular dynamics with the stochastic process provides a convenient way to compute structural and thermodynamic properties of chemical, biological, and materials systems. It is demonstrated that the virtual dynamics case that we proposed…
General discrete one-dimensional stochastic models to describe the transport of single molecules along coupled parallel lattices with period $N$ are developed. Theoretical analysis that allows to calculate explicitly the steady-state…
We extend the work of Tanase-Nicola and Kurchan on the structure of diffusion processes and the associated supersymmetry algebra by examining the responses of a simple statistical system to external disturbances of various kinds. We…
Interactions between biomolecules, electrons and protons are essential to many fundamental processes sustaining life. It is therefore of interest to build mathematical models of these bioelectrical processes not only to enhance…
A stochastic deformation of a thermodynamic symplectic structure is studied. The stochastic deformation procedure is analogous to the deformation of an algebra of observables like deformation quantization, but for an imaginary deformation…
In this review we focus on the idea of establishing connections between the mechanical properties of DNAligand complexes and the physical chemistry of DNA-ligand interactions. This type of connection is interesting because it opens the…
Elastomers are used in a wide range of applications because of their large strain to failure, low density, and tailorable stiffness and toughness. The mechanical behavior of elastomers derives mainly from the entropic elasticity of the…
Heterogeneity in biological molecules, resulting in molecule-to-molecule variations in their dynamics and function, is an emerging theme. To elucidate the consequences of heterogeneous behavior at the single molecule level, we propose an…