Related papers: Modeling single-molecule stretching experiments us…
Heat conduction in one-dimensional (1D) systems is studied based on an analytical S-matrix method, which is developed in the mesoscopic electronic transport theory and molecular dynamic (MD) simulations. It is found that heat conduction in…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
The paper analyses stochastic systems describing reacting molecular systems with a combination of two types of state spaces, a finite-dimensional, and an infinite dimenional part. As a typical situation consider the interaction of larger…
In order to increase the efficiency of the computer simulation of biological molecules, it is very common to impose holonomic constraints on the fastest degrees of freedom; normally bond lengths, but also possibly bond angles. However, as…
In this work we study, at the single molecular level, the thermodynamic and dynamic characteristics of an enzymatic reaction comprising a rate limiting step. We investigate how the stability of the enzyme-state stationary probability…
Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force vs. displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession…
Single-molecule force spectroscopy has proven to be a powerful tool for studying the kinetic behavior of biomolecules. Through application of an external force, conformational states with small or transient populations can be stabilized,…
Multivalent associative proteins with strong complementary interactions play a crucial role in phase separation of intracellular liquid condensates. We study the internal dynamics of such "bond-network" condensates comprised of two…
Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…
Predicting the macroscopic mechanical behavior of polymeric materials from the micro-structural features has remained a challenge for decades. Existing theoretical models often fail to accurately capture the experimental data, due to…
We study the role of active coupling on the transport properties of homogeneously charged macromolecules in an infinitely dilute solution. An enzyme becomes actively bound to a segment of the macromolecule, exerting an electrostatic force…
This review is a simplified summary of the thermodynamic dislocation theory, with special emphasis on the role of an effective temperature. Materials scientists, for decades, have asserted that statistical thermodynamics is not applicable…
A tight binding model for scanning tunneling microscopy images of a molecule adsorbed on a metal surface is described. The model is similar in spirit to that used to analyze conduction along molecular wires connecting two metal leads and…
In typical single-molecule force spectroscopy experiments the mechanical unfolding of molecular complexes or biomolecules is studied applying a force ramp to one end of the system while the other end is kept fixed in space. The…
We study thermodynamic processes in contact with a heat bath that may have an arbitrary time-varying periodic temperature profile. Within the framework of stochastic thermodynamics, and for models of thermo-dynamic engines in the idealized…
Single-molecule biophysics has transformed our understanding of the fundamental molecular processes involved in living biological systems, but also of the fascinating physics of life. Far more exotic than a collection of exemplars of soft…
The exact study of small systems can guide us toward measures for extracting information about many-body physics as we move to more complex systems capable of quantum information processing or quantum analog simulation. We use exact…
The paper gives an account of a detailed investigation of the thermodynamic branch as a path of the chemical system deviation from its isolated thermodynamic equilibrium under an external impact. For a combination of direct and reverse…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
Thermodynamics can be formulated in either of two approaches, the phenomenological approach, which refers to the macroscopic properties of systems, and the statistical approach, which describes systems in terms of their microscopic…