Related papers: Synchronized Pivots
More advanced visualization tools are needed to assist with the analyses and interpretation of human metabolomics data, which are rapidly increasing in quantity and complexity. Using a dataset of several hundred bioactive lipid metabolites…
We study properties of a piecewise deterministic Markov process modeling the changes in concentration of specific antibodies. The evolution of densities of the process is described by a stochastic semigroup. The long-time behaviour of this…
This paper investigates the non-equilibrium hydrodynamic behavior of a simple totally asymmetric interacting particle system of particles, antiparticles and holes on $\mathbb{Z}$. Rigorous hydrodynamic results apply to our model with a…
Many thermodynamic instabilities in one dimension (e.g. DNA thermal denaturation, wetting of interfaces) can be described in terms of simple models involving harmonic coupling between nearest neighbors and an asymmetric on-site potential…
Sampling from flat energy or density distributions has proven useful in equilibrating complex systems with large energy barriers. Several thermostats and barostats are presented to sample these flat distributions by molecular dynamics.…
We investigate the dynamics of micron-scale drops pushed across a hydrophobic or superhydrophobic surface. The velocity profile across the drop varies from quadratic to linear with increasing height, indicating a crossover from a sliding to…
We combine the standard 1992 20x20 substitution matrix based on block alignment, BLOSUM62, with the standard 1982 amino acid hydropathicity scale KD as well as the modern 2007 hydropathicity scale MZ, and compare the results. The…
This review focuses on the striking recent progress in solving for hydrophobic interactions between small inert molecules. We discuss several new understandings. Firstly, the _inverse _temperature phenomenology of hydrophobic interactions,…
We introduce a polymer model where the transition from swollen to compact configurations is due to interactions between the monomers and the solvent. These interactions are the origin of the effective attractive interactions between…
In this work we employ various methods of analysis (unfolding simulations and comparative analysis of structures and sequences of proteomes of thermophilic organisms) to show that organisms can follow two major strategies of thermophilic…
We study a totally asymmetric simple exclusion process where jumps happen at rate one, except at the origin where the rate is lower. We prove a hydrodynamic scaling limit to a macroscopic profile described by a variational formula. The…
Multi-particle collision dynamics is an appealing numerical technique aiming at simulating fluids at the mesoscopic scale. It considers molecular details in a coarse-grained fashion and reproduces hydrodynamic phenomena. Here, the…
An overview of theoretical results and experimental data on the thermodynamics, structure and dynamics of the heterophase glass-forming liquids is presented. The theoretical approach is based on the mesoscopic heterophase fluctuations model…
In suitable environments, proteins, nucleic acids and certain synthetic polymers fold into unique conformations. This work shows that it is possible to construct lattice models of foldable heteropolymers by expressing the energy only in…
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…
As an example of topic where biology and physics meet, we present the issue of protein folding and stability, and the development of thermodynamics-based bioinformatics tools that predict the stability and thermal resistance of proteins and…
We present the multiscale entropy analysis of short term physiological time series of simultaneously acquired samples of heart rate, blood pressure and lung volume, from healthy subjects and from subjects with Chronic Heart Failure.…
Any interface boundary in an equilibrium system of Coulomb particles is accompanied by the existence of a finite difference in the average electrostatic potential through this boundary. The discussed interface potential drop is a…
Molecular dynamics simulations have revealed a dramatic increase, with increasing temperature, of the amplitude of electrostatic fluctuations caused by water at the active site of metalloprotein plastocyanin. The increased breadth of…
Hydrodynamic slippage plays a crucial role in the flow dynamics of thin polymer films, as recently shown by the analysis of the profiles of liquid fronts. For long-chained polymer films it was reported that a deviation from a symmetric…