All posts under category "Condensed Matter / Cond-Mat.soft"
We examine the effective counterion-mediated electrostatic interaction between two like-charged dielectric cylinders immersed in a continuous dielectric medium containing neutralizing mobile counterions. We focus on the effects of image charges induced as a result of the dielectric mismatch between
Using a recently developed mesoscopic theory of protein dielectrics, we have calculated the salt bridge energies, total residue electrostatic potential energies, and transfer energies into a low dielectric amyloid-like phase for 12 species and mutants of the prion protein. Salt bridges and self ener
Recent studies have shown the possibility of water transport across carbon nanotubes, even in the case of nanotubes with small diameter (0.822 nm). In this case, water shows subcontinuum transport following an ordered 1D structure stabilized by hydrogen bonds. In this work, we report MD simulations
We revisit the classical problem of nucleated polymerisation and derive a range of exact results describing polymerisation in systems intermediate between the well-known limiting cases of a reaction starting from purely soluble material and for a reaction where no new growth nuclei are formed.
The influence of a single walled carbon nanotube on the structure of a cholesterol cluster (domain) developed over the surface of the endothelial protein 1LQV has been investigated using the classical molecular dynamics (MD) simulation technique. We have observed a substantial impact of carbon nanot
Dense granular flows exhibit nonlocal effects due to stress transmission in microplastic events, especially in quasi-static or slowly sheared regions. Hence, traditional local rheological models fail to capture spatial cooperativity effects that are prominent in many granular systems. The nonlocal g
In this informal report, I outline my research efforts, collaborations, and other experiences while participating in the Naval Research Laboratory (NRL)'s Advanced Graduate Research Program (AGRP), aka Sabbatical, from October 2008 through September 2009. This report is in no way intended to present
We extend the event-chain Monte Carlo algorithm from hard-sphere interactions to the micro-canonical ensemble (constant potential energy) for general potentials. This event-driven Monte Carlo algorithm is non-local, rejection-free, and allows for the breaking of detailed balance. The algorithm uses
By exerting mechanical force it is possible to unfold/refold RNA molecules one at a time. In a small range of forces, an RNA molecule can hop between the folded and the unfolded state with force-dependent kinetic rates. Here, we introduce a mesoscopic model to analyze the hopping kinetics of RNA hai
For compressible fluids under shock wave reaction, we have proposed two Multiple-Relaxation-Time (MRT) Lattice Boltzmann (LB) models [F. Chen, et al, EPL textbf{90} (2010) 54003; Phys. Lett. A textbf{375} (2011) 2129.]. In this paper, we construct a new MRT Lattice Boltzmann model which is not only
Active networks composed of biopolymers and motor proteins provide versatile biomimetic systems that have advanced active matter physics and deepened our understanding of cytoskeletal dynamics and self-organization under diverse stimuli. In these systems, activity arises in aqueous solutions where m
During the synthesis of integral membrane proteins (IMPs), the hydrophobic amino acids of the polypeptide sequence are partitioned mostly into the membrane interior and hydrophilic amino acids mostly into the aqueous exterior. We analyze the minimum free energy state of polypeptide sequences partiti
Experimental variables of optical tweezers instrumentation that affect RNA folding/unfolding kinetics were investigated. A model RNA hairpin, P5ab, was attached to two micron-sized beads through hybrid RNA/DNA handles; one bead was trapped by dual-beam lasers and the other was held by a micropipette
Conformational fluctuations are believed to play an important role in the process by which transcription factor proteins locate and bind their target site on the genome of a bacterium. Using a simple model, we show that the binding time can be minimized, under selective pressure, by adjusting the sp
The eye lens is the most characteristic example of mammalian tissues exhibiting complex colloidal behaviour. In this paper we briefly describe how dynamics in colloidal suspensions can help addressing selected aspects of lens cataract which is ultimately related to the protein self-assembly under pa
This article describes the design and manufacturing of a microfluidic chip, allowing for the actuation of a gas-liquid interface and of the neighboring fluid. A first way to control the interface motion is to apply a pressure difference across it. In this case, the efficiency of three different micr
We consider a simple working hypothesis that all permeation properties of open ionic channels can be predicted by understanding electrodiffusion in fixed structures, without invoking conformation changes, or changes in chemical bonds. We know, of course, that ions can bind to specific protein struct
We present a simple and emph{non-invasive} experimental procedure to measure the linear viscoelastic properties of cells by passive video particle tracking microrheology. In order to do this, a generalised Langevin equation is adopted to relate the time-dependent thermal fluctuations of a bead, chem
In this paper, we analyze the electrotactic movement of Dictyostelium discoideum from the viewpoint of non-equilibrium statistical mechanics. Because we can observe fluctuating behavior of cellular trajectories, we analyze the probability distribution of the trajectories with the aid of the fluctuat
Nuclear pore complexes (NPCs) are very selective filters that monitor the transport between the cytoplasm and the nucleoplasm. Two models have been suggested for the plug of the NPC. They are (i) it is a reversible hydrogel or (ii) it is a polymer brush. We propose a mesoscopic model for the transpo
We study the passage times of a translocating polymer of length $N$ in three dimensions, while it is pulled through a narrow pore with a constant force $F$ applied to one end of the polymer. At small to moderate forces, satisfying the condition $FN^{nu}/k_BTlesssim1$, where $nuapprox0.588$ is the Fl
The ability of cells to undergo reversible shape changes is often crucial to their survival. For Red Blood Cells (RBCs), irreversible alteration of the cell shape and flexibility often causes anemia. Here we show theoretically that RBCs may react irreversibly to mechanical perturbations because of t
Soil liquefaction is a significant natural hazard associated with earthquakes. Some of its devastating effects include tilting and sinking of buildings and bridges, and destruction of pipelines. Conventional geotechnical engineering practice assumes liquefaction occurs via shear-driven compaction an
Aggregates of twisted protein fibers, such as sickle hemoglobin and actin, are important examples of biopolymers in which elastic interactions play a crucial role in determining the (metastable) bundle radii. Here, we present a corrected version of analysis on the stability of sickle hemoglobin fibe
The large class of moving boundary processes in the plane modeled by the so-called Laplacian growth, which describes, e.g., solidification, electrodeposition, viscous fingering, bacterial growth, etc., is known to be integrable and to exhibit a large number of exact solutions. In this work, the boun
Morphological instabilities of growing tissues that impinge on passive materials are typical of invasive cancers. To explain these instabilities in experiments on breast epithelial spheroids in an extracellular matrix, we develop a continuum phase field model of a growing active liquid expanding int
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