Related papers: A Two-Step Biopolymer Nucleation Model Shows a Non…
The formation of various bicontinuous phases from binary blends of linear AB diblock copolymers (DBCPs) is studied using the polymeric self-consistent field theory. The theoretical study predicts that the double-diamond and the "plumber's…
Protein oligomers have been implicated as toxic agents in a wide range of amyloid-related diseases. Yet it has remained unsolved whether the oligomers are a necessary step in the formation of amyloid fibrils, or just a dangerous by-product.…
Based on classical nucleation theory, we propose a couple of theoretical models for the nucleation of polymer crystallization, i.e. one for a single chain system (Model S) and the other for a multi-chain system (Model M). In these models,…
Computational modeling of assembly is challenging for many systems because their timescales vastly exceed those accessible to simulations. This article describes the MultiMSM, which is a general framework that uses Markov state models…
Nucleation and growth is the dominant relaxation mechanism driving first order phase transitions. In two-dimensional at systems nucleation has been applied to a wide range of problems in physics, chemistry and biology. Here we study…
A simple phenomenological model for describing the conformational dynamics of biological macromolecules via the nonlinearity-induced instabilities is proposed. It is shown that the interaction between charges and bending degrees of freedom…
Biological polymers, such as intrinsically disordered proteins, play a central role in cellular biology, including mediating phase separation and controlling activity of biological condensates. The physical properties and functions of…
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Langevin molecular dynamics (MD) with a mesoscopic lattice Boltzmann (LB) method for the…
A nonequilibrium molecular dynamics computer simulation on microsegregated solutions of symmetrical diblock copolymers is reported. As the polymer concentration increases, the system undergoes phase transitions in the following order: body…
This thesis can be divided into two independent parts. In the first part of this thesis, we focus on studying the kinetic pathways of nucleation in colloidal systems. In Chapter 2, we briefly introduce the relevant theory of nucleation,…
Unlike fluids at thermal equilibrium, biomolecular mixtures in living systems can sustain nonequilibrium steady states, in which active processes modify the conformational states of the constituent molecules. Despite qualitative…
The biopolymers actin and microtubules are often in an ongoing assembling/disassembling state far from thermal equilibrium. Above a critical density this leads to spatially periodic patterns, as shown by a scaling argument and in terms of a…
Molecular dynamics computer simulations are used to investigate thedynamics of a binary mixture of charged (Yukawa) particles with a size-ratio of 1:5. We find that the system undergoes a phase transition where the large particles…
The kinetics of nucleation of a core-shell composite nucleus that consists of a core of stable final phase surrounded by a wetting layer of intermediate metastable phase is studied using the kinetic theory of binary nucleation not only in…
We study a three species monomer-monomer catalytic surface reaction model with a reactive steady state bordered by three equivalent unreactive phases where the surface is saturated with one species. The transition from the reactive to a…
Nucleation is a key step in the synthesis of new material from solution. Well-established lattice-gas models can be used to gain insight into the basic physics of nucleation pathways involving a single nucleus type. In many situations a…
Several neurological disorders are associated with the aggregation of aberrant proteins, often localized in intracellular organelles such as the endoplasmic reticulum. Here we study protein aggregation kinetics by mean-field reactions and…
In this paper, we investigate a stochastic model describing the time evolution of a polymerization process. A polymer is a macro-molecule resulting from the aggregation of several elementary sub-units called monomers. Polymers can grow by…
In many biopolymer solutions, attractive interactions that stabilize finite-sized clusters at low concentrations also promote phase separation at high concentrations. Here we study a model biopolymer system that exhibits the opposite…
A novel assay based on micropatterning and time-lapse microscopy has been developed for the study of nuclear migration dynamics in cultured mammalian cells. When cultured on 10-20 um wide adhesive stripes, the motility of C6 glioma and…