Related papers: Dynamics of unfolded protein aggregation
Protein folding and evolution are intimately linked phenomena. Here, we revisit the concept of exons as potential protein folding modules across 38 abundant and conserved protein families. Taking advantage of genomic exon-intron…
The Poisson-binomial distribution is useful in many applied problems in engineering, actuarial science, and data mining. The Poisson-binomial distribution models the distribution of the sum of independent but not identically distributed…
Understanding the time evolution of fragmented animal populations and their habitats, connected by migration, is a problem of both theoretical and practical interest. This paper presents a method for calculating the time evolution of the…
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 biophysics, the search for analytical solutions of stochastic models of cellular processes is often a challenging task. In recent work on models of gene expression, it was shown that a mapping based on partitioning of Poisson arrivals…
In the present work, we review the fundamental methods which have been developed in the last few years for classifying into families and clans the distribution of amino acids in protein databases. This is done through functions of random…
Protein aggregation is of particular interest due to its connection with many diseases and disorders. Many factors can alter the dynamics and result of this process, one of them being the diffusivity of the monomers and aggregates in the…
We study the non-stationary Feller process with time varying coefficients. We obtain the exact probability distribution exemplified by its characteristic function and cumulants. In some particular cases we exactly invert the distribution…
The information regarding the structure of a single protein is encoded in the network of interacting amino acids. Considering each protein as a weighted and unweighted network of amino acids we have analyzed a total of forty nine protein…
A stochastic model of autoregulated bursty gene expression by Kumar et al. [Phys. Rev. Lett. 113, 268105 (2014)] has been exactly solved in steady-state conditions under the implicit assumption that protein numbers are sufficiently large…
Excess hazard modeling is one of the main tools in population-based cancer survival research. Indeed, this setting allows for direct modeling of the survival due to cancer even in the absence of reliable information on the cause of death,…
Protein aggregation on the plasma membrane (PM) is of critical importance to many cellular processes such as cell adhesion, endocytosis, fibrillar conformation, and vesicle transport. Lateral diffusion of protein aggregates or clusters on…
Neurodegenerative diseases are driven by the accumulation of protein aggregates in the brain of affected individuals. The aggregation behaviour in vitro is well understood and driven by the equilibration of a super-saturated protein…
The normal distribution is used as a unified probability distribution, however, our researcher found that it is not good agreed with the real-life dynamical system's data. We collected and analyzed representative naturally occurring data…
The recently proposed fluctuation relation in unfolding forces [Phys. Rev. E ${\bf 84}$, $060101$(R) $(2011)$] is re-examined taking into account the explicit time dependence of the force distribution. The stretching of a tethered Rouse…
From a systems biology perspective the majority of cancer models, although interesting and providing a qualitative explanation of some problems, have a major disadvantage in that they usually miss a genuine connection with experimental…
We consider the problem of estimating the missing mass, partition function or evidence and its probability distribution in the case that for each sample point in the discrete sample space its (unnormalized) probability mass is revealed.…
Mechanical stretching of six proteins is studied through molecular dynamics simulations. The model is Go-like, with Lennard-Jones interactions at native contacts. Low temperature unfolding scenarios are remarkably complex and sensitive to…
Anomalous diffusion is an established phenomenon but still a theoretical challenge in non-equilibrium statistical mechanics. Physical models are built incrementally, and the most recent and most general family is based on the fractional…
We propose a general theory to describe the distribution of protein-folding transition paths. We show that transition paths follow a predictable sequence of high-free-energy transient states that are separated by free-energy barriers. Each…