Related papers: Recurrence quantification analysis as a tool for t…
In the context of Wilsonian Renormalization, renormalization group (RG) flows are a set of differential equations that defines how the coupling constants of a theory depend on an energy scale. These equations closely resemble…
Comments: 6 pages RevTeX, 6 Postscript figures. We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water…
We develop a unified spectral-semigroup framework that connects real-time and imaginary-time quantum dynamics through analytic continuation. Within this formulation, evolution is expressed as an exponential reweighting of spectral…
Soft condensed matter structures often challenge us with complex many-body phenomena governed by collective modes spanning wide spatial and temporal domains. In order to successfully tackle such problems mesoscopic coarse-grained (CG)…
Phantom systems consisting of liposome suspensions are widely employed to investigate quantitative MRI parameters mimicking cellular membranes. The proper physical understanding of the measurement results, however, requires proper models…
We consider a suspension of active rigid particles (swimmers) in a steady Stokes flow, where particles are distributed according to a stationary ergodic random process, and we study its homogenization in the macroscopic limit. A key point…
The interface between hemoglobin (Hb) and its environment, in particular water, is of great physiological relevance. Here, results from {\it in vitro}, {\it in vivo}, and computational experiments (molecular dynamics simulations) are…
We perform lengthy molecular dynamics simulations of the SPC/E model of water to investigate the dynamics under pressure at many temperatures and compare with experimental measurements. We calculate the isochrones of the diffusion constant…
This work presents a systematic methodology for describing the transient dynamics of coarse-grained molecular systems inferred from all-atom simulated data. We suggest Langevin-type dynamics where the coarse-grained interaction potential…
Lithium chloride LiCl is widely used as a prototype system to study the strongly dissociated 1-1 electrolyte solution. Here, we combined experimental measurements and classical molecular dynamics simulations to study the ion conduction in…
We use molecular dynamics simulation results on viscous binary Lennard-Jones mixtures to examine the correlation between the potential energy and the virial. In accord with a recent proposal [U. R. Pedersen et. al. Phys. Rev. Lett. 100,…
A systematic comparison was carried out to assess the influence of representative thermostat methods in constant-temperature molecular dynamics simulations. The thermostat schemes considered include the Nos\'e--Hoover thermostat and its…
Although liquid water has been studied for many decades by (X-ray and neutron) diffraction measurements, new experimental results keep appearing, virtually every year. The reason for this is that neither X-ray, nor neutron diffraction data…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
We present simulations of stochastic fluid dynamics in the vicinity of a critical endpoint belonging to the universality class of the Ising model. This study is motivated by the challenge of modeling the dynamics of critical fluctuations…
Recurrence plot based measures of complexity are capable tools for characterizing complex dynamics. In this letter we show the potential of selected recurrence plot measures for the investigation of even high-dimensional dynamics. We apply…
We investigate the hydrodynamic properties of a fluid simulated with a mesoscopic solvent model. Two distinct regimes are identified, the `particle regime' in which the dynamics is gas-like, and the `collective regime' where the dynamics is…
Biological membranes are host to proteins and molecules which may form domain-like structures resulting in spatially-varying material properties. Vesicles with such heterogeneous membranes can exhibit intricate shapes at equilibrium and…
Despite the simplicity of its molecular unit, water is a challenging system because of its uniquely rich polymorphism and predicted but yet unconfirmed features. Introducing a novel space of generalized coordinates that capture changes in…
Recurrence analysis is a well settled method allowing to discern chaos from order, and determinism from noise. We apply this tool to study time series representing geodesic and inspiraling motion of a test particle in a deformed Kerr…