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The use of ultra-thin, i.e., monolayer films plays an important role for the emerging field of nano-fluidics. Since the dynamics of such films is governed by the interplay between substrate-fluid and fluid-fluid interactions, the transport…
The depletion interaction mediated by non-adsorbing polymers promotes condensation and assembly of repulsive colloidal particles into diverse higher-order structures and materials. One example, with particularly rich emergent behaviors, is…
In recent years, fluorescence correlation spectroscopy has been increasingly applied for the study of polymer dynamics on the nanometer scale. The core idea is to extract, from a measured autocorrelation curve, an effective mean-square…
Protein nanoclustering is a characteristic feature of their activated state and is essential for forming numerous subcellular structures. The formation of these nanoclusters is highly dependent on a series of post-translational…
To understand the role of collective motion in the often large changes in interfacial molecular mobility observed in polymer films, we investigate the extent of collective motion in the interfacial regions of a thin supported polymer film…
Contact inhibition plays a crucial role in the motility of cells, the process of wound healing, and the formation of tumors. By mimicking the mechanical motion of calls crawling on a substrate using a pseudopod, we constructed a minimal…
In active matter systems, self-propelled particles can self-organize to undergo collective motion, leading to persistent dynamical behavior out of equilibrium. In cells, cytoskeletal filaments and motor proteins self-organize into complex…
Modeling approaches of suspended, rod-like particles and recent experimental data have shown that depletion forces display different signatures depending on the orientation of these particles. It has been shown that axial attraction of two…
Collective behavior of proteins on biomembranes is usually studied within the spontaneous curvature model. Here we consider an alternative phenomenological approach, which accounts consistently for partial ordering of proteins as well as…
Proteins often exhibit subdiffusive configurational dynamics. The origins of this subdiffusion are still unresolved. We investigate the impact of non-Markovian friction and the free energy landscape on the dynamics of fast-folding proteins…
Understanding particle motion in narrow channels is essential to guide progress in numerous applications, from filtration to vascular transport. Thermal or active fluctuations of channel walls for fluid-filled channels can slow down or…
We study a strongly interacting crowded system of self-propelled stiff filaments by event-driven Brownian dynamics simulations and an analytical theory to elucidate the intricate interplay of crowding and self-propulsion. We find a…
Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating postulated interaction schemes for a set of…
The study of active matter system has critical importance in revealing the physical essence of biological collective behavior. Dense bacterial suspension - a typical biological active matter, exhibits a wide range of phenomenons, among…
Experiments measuring contact formation between a probe and quencher in disordered chains provide information on the fundamental dynamical timescales relevant to protein folding, but their interpretation usually relies on simplified…
The kinetic processes in nanoparticle-based catalysis are dominated by large fluctuations and spatiotemporal heterogeneities, in particular for diffusion-influenced reactions which are far from equilibrium. Here, we report results from…
Enzymatic ligation is essential for the synthesis of long DNA. However, the number of ligated products exponentially decays as the DNA synthesis proceeds in a random manner. The controlling of ligation randomness is of importance to…
While experiments and computer simulations to study biological phenomena are usually performed in diluted in vitro conditions, such phenomena happen inside the cell, an environment densely packed with diverse macromolecules. Here, we revise…
Density-dependent diffusion is a widespread phenomenon in nature. We have examined the density-dependent diffusion behavior of some biological processes such as tumor growth and invasion [23]. Here, we extend our previous work by developing…
Cell division, aging, and stress recovery triggers spatial reorganization of cellular components in the cytoplasm, including membrane bound organelles, with molecular changes in their compositions and structures. However, it is not clear…