Related papers: Synchronized Pivots
The scale invariance of natural images suggests an analogy to the statistical mechanics of physical systems at a critical point. Here we examine the distribution of pixels in small image patches and show how to construct the corresponding…
We present results of Monte Carlo computer simulations of a coarse-grained hydrophobic-polar Go-like heteropolymer model and discuss thermodynamic properties and kinetics of an exemplified heteropolymer, exhibiting two-state folding…
We employ a mesoscopic model for studying aggregation processes of protein-like hydrophobic-polar heteropolymers. By means of multicanonical Monte Carlo computer simulations, we find strong indications that peptide aggregation is a phase…
In this paper we consider the effect of surface heterogeneity on the slippage of fluid, using two complementary approaches. First, MD simulations of a corrugated hydrophobic surface have been performed. A dewetting transition, leading to a…
Hydrophobicity is thought to be one of the primary forces driving the folding of proteins. On average, hydrophobic residues occur preferentially in the core, whereas polar residues tends to occur at the surface of a folded protein. By…
We consider a harmonic oscillator under periodic driving and coupled to two harmonic-oscillator heat baths at different temperatures. We use the thermofield transformation with chain mapping for this setup, which allows us to study the…
In this manuscript, we present a general computational method for characterizing the molecular structure of liquid water interfaces as sampled from atomistic simulations. With this method, the interfacial structure is quantified based on…
We study a single statistical amphiphilic copolymer chain AB in a selective solvent (e.g.water). Two situations are considered. In the annealed case, hydrophilic (A) and hydrophobic (B) monomers are at local chemical equilibrium and both…
Based on a recently introduced analytical strategy [Hollingshead et al., J. Chem. Phys. 139, 161102 (2013)], we present a web applet that can quickly and semi-quantitatively estimate the equilibrium radial distribution function and related…
The growing need for creating surfaces with specific wetting properties, such as superhyrdophobic behavior, asks for novel methods for their efficient design. In this work, a fast computational method for the evaluation of patterned…
From dumbbells to FCC crystals, we study the self-assembly pathway of amphiphatic, spherical colloidal particles as a function of the size of the hydrophobic region using molecular dynamics simulations. Specifically, we analyze how local…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…
Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we…
Deviation of blood flow from an optimal range is known to be associated with the initiation and progression of vascular pathologies. Important open questions remain about how the abnormal flow drives specific wall changes in pathologies…
We present a multiparticle collision dynamics (MPC) implementation of layered immiscible fluids $A$ and $B$ of different shear viscosities separated by planar interfaces. The simulated flow profile for imposed steady shear motion and the…
Amphiphiles are molecules which have both hydrophilic and hydrophobic parts. In water- and/or oil-like solvent, they self-assemble into extended sheet-like structures due to the hydrophobic effect. The free energy of an amphiphilic system…
We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bacterium and one from a mesophilic organism; three are in the…
This thesis investigates the interactions of different degrees of freedom of one joint system within the theory of stochastic thermodynamics. First, a comprehensive introduction to the subjects of stochastic processes, information theory…
Density profiles are the most common measure of inhomogeneous structure in confined fluids, but their connection to transport coefficients is poorly understood. We explore via simulation how tuning particle-wall interactions to flatten or…
This paper analyzes a simplified model of viral infection and evolution using the 'grand canonical ensemble' and formalisms from statistical mechanics and thermodynamics to enumerate all possible viruses and to derive thermodynamic…