Related papers: Efficient methods for determining folding free ene…
This work addresses the question of whether it is possible to define simple pair-wise interaction terms to approximate free energies of proteins or polymers. Rather than ask how reliable a potential of mean force is, one can ask how…
Biomolecules carry out very specialized tasks inside the cell where energies involved are few tens of k_BT, small enough for thermal fluctuations to be relevant in many biomolecular processes. In this paper I discuss a few concepts and…
Monte Carlo computer simulations are used to study the conformational free energy of a folded polymer confined to a long cylindrical tube. The polymer is modeled as a hard-sphere chain. Its conformational free energy $F$ is measured as a…
We present a detailed comparison of computational efficiency and precision for several free energy difference ($\Delta F$) methods. The analysis includes both equilibrium and non-equilibrium approaches, and distinguishes between…
Using numerical modeling we study emergence of structure and structure-related nonlinear conduction properties in the self-assembled nanoparticle films. Particularly, we show how different nanoparticle networks emerge within assembly…
The stochastic dynamics of small elastic objects in fluid are central to many important and emerging technologies. It is now possible to measure and use the higher modes of motion of elastic structures when driven by Brownian motion alone.…
The stochastic differential equations for a model of dissipative particle dynamics, with both total energy and total momentum conservation at every time-step, are presented. The algorithm satisfies detailed balance as well as the…
A new molecular dynamics model in which the point charges on atomic sites are allowed to fluctuate in response to the environment is developed and applied to water. The idea for treating charges as variables is based on the concept of…
Examples of self propulsion in strongly fluctuating environment is abound in nature, e.g., molecular motors and pumps operating in living cells. Starting from Langevin equation of motion, we develop a fluctuating thermodynamic description…
We propose a new method to analyze fluctuations in the strength function phenomena in highly excited nuclei. Extending the method of multifractal analysis to the cases where the strength fluctuations do not obey power scaling laws, we…
We use nonequilibrium molecular dynamics simulations to verify recent tube-model predictions that associative polymer networks exhibit broad stretch fluctuations during elongational flow. Simulations further show that these fluctuating…
We compare efforts to extract self energies and fluctuation spectra of the cuprates using optical and photoemission techniques. The fluctuations have contributions from both the coherent and incoherent parts of the band, which are spread…
A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…
The forced rupture of single chemical bonds under external load is addressed. A general framework is put forward to optimally utilize the experimentally observed rupture force data for estimating the parameters of a theoretical model. As an…
Fluctuations in the large-scale structure of the Universe contain significant information about cosmological physics, but are modulated in survey datasets by various observational effects. Building on existing literature, we provide a…
Heat, work and entropy production: the statistical distribution of such quantities are constrained by the fluctuation theorems (FT), which reveal crucial properties about the nature of non-equilibrium dynamics. In this paper we report…
We derive a fluctuation theorem for generalized work distributions, related to bijective mappings of the phase spaces of two physical systems, and use it to derive a two-sided constraint maximum likelihood estimator of their free energy…
We compute the growth fluctuations in equilibrium of a wide class of deposition models. These models also serve as general frame to several nearest-neighbor particle jump processes, e.g. the simple exclusion or the zero range process, where…
Protein folding is a universal process, very fast and accurate, which works consistently (as it should be) in a wide range of physiological conditions. The present work is based on three premises, namely: ($i$) folding reaction is a process…
Investigations of molecular bonds between single molecules and molecular complexes by the dynamic force spectroscopy are subject to large fluctuations at nanoscale and possible other aspecific binding, which mask the experimental output.…