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Phase-separated biomolecular condensates containing proteins and RNAs can assemble into higher-order structures by forming thermodynamically stable interfaces between immiscible phases. Using a minimal model of a protein/RNA interaction…
The interactions between diffusing molecules and membrane-bound receptors drive numerous cellular processes. In this work, we develop a spatial model of molecular interactions with membrane receptors by homogenizing the cell membrane and…
Over the years, advances in experimental and computational methods have helped us to understand the role of thermodynamic, kinetic and active (chaperone-aided) effects in coordinating the folding steps required to achieving a knotted native…
Phase separation has emerged as an essential concept for the spatial organization inside biological cells. However, despite the clear relevance to virtually all physiological functions, we understand surprisingly little about what phases…
Protein folding is a phenomenon that has been studied for about 50 years and still remains as an unsolved problem. The main feature of this process is that it occurs as an all or none process, so a protein, can jump directly between folded…
Movement within eukaryotic cells largely originates from localized forces exerted by myosin motors on scaffolds of actin filaments. Although individual motors locally exert both contractile and extensile forces, large actomyosin structures…
Biofilament-motor protein complexes are ubiquitous in biology and drive the transport of cargo vital for many fundamental cellular processes. As they move, motor proteins exert compressive forces on the filaments to which they are attached,…
We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…
Protein structure prediction and folding are fundamental to understanding biology, with recent deep learning advances reshaping the field. Diffusion-based generative models have revolutionized protein design, enabling the creation of novel…
Synthetic genetic circuits are implemented in living cells for their operation. During gene expression, proteins are produced from the respective genes, by formation of complexes through the process of transcription and translation. In…
The structure of molecular networks derives from dynamical processes on evolutionary time scales. For protein interaction networks, global statistical features of their structure can now be inferred consistently from several…
It is well known that many biochemical processes in the cell such as gene regulation, growth signals and activation of ion channels, rely on mechanical stimuli. However, the mechanism by which mechanical signals propagate through cells is…
Genes with similar transcriptional activation kinetics can display very different temporal mRNA profiles due to differences in transcription time, degradation rate and RNA processing kinetics. Recent studies have shown that a…
The diffusion-controlled limit of reaction times for site-specific DNA-binding proteins is derived from first principles. We follow the generally accepted concept that a protein propagates via two competitive modes, a three-dimensional…
Signaling in enzymatic networks is typically triggered by environmental fluctuations, resulting in a series of stochastic chemical reactions, leading to corruption of the signal by noise. For example, information flow is initiated by…
In this paper, we propose adding enzymes to the propagation environment of a diffusive molecular communication system as a strategy for mitigating intersymbol interference. The enzymes form reaction intermediates with information molecules…
We formulate a kinetic model of DNA replication that quantitatively describes recent results on DNA replication in the in vitro system of Xenopus laevis prior to the mid-blastula transition. The model describes well a large amount of…
We propose a physical model for developmental process at cellular level to discuss the mechanism of epigenetic landscape. In our simplified model, a minimal model, the network of the interaction among cells generates the landscape…
We show how to construct a reduced description of interacting genes in noisy, small regulatory networks using coupled binary "spin" variables. Treating both the protein number and gene expression state variables stochastically and on equal…
Motor enzymes are remarkable molecular machines that use the energy derived from the hydrolysis of a nucleoside triphosphate to generate mechanical movement, achieved through different steps that constitute their kinetic cycle. These…