Related papers: Pathways for virus assembly around nucleic acids
The self-assembly of anisotropic building blocks into complex spatial architectures is an important design strategy in material science but the mechanisms by which the anisotropic interactions influence the early-stage growth and formation…
As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment, and assembly.…
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 develop a path-based approach to continuous-time random walks on networks with arbitrarily weighted edges. We describe an efficient numerical algorithm for calculating statistical properties of the stochastic path ensemble. After…
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…
Proteins are an important class of biomolecules that serve as essential building blocks of the cells. Their three-dimensional structures are responsible for their functions. In this thesis we have investigated the protein structures using a…
We introduce a method for predicting RNA folding pathways, with an application to the most important RNA tetraloops. The method is based on the idea that ensembles of three-dimensional fragments extracted from high-resolution crystal…
We propose a machine-learning method for evaluating the potential barrier governing atomic transport based on the preferential selection of dominant points for the atomic transport. The proposed method generates numerous random samples of…
We use computer simulation to study crystal-forming model proteins equipped with interactions that are both orientationally specific and nonspecific. Distinct dynamical pathways of crystal formation can be selected by tuning the strengths…
A phase field model with two phase fields, representing the concentration and the head-tail separation of amphiphilic molecules, respectively, has been constructed using an extension of the Ohta-Kawasaki model (Macromolecules 19, 2621-2632…
We show that macro-molecular self-assembly can recognize and classify high-dimensional patterns in the concentrations of $N$ distinct molecular species. Similar to associative neural networks, the recognition here leverages dynamical…
The intrinsic property of proteins to form structural motifs such as alpha-helices and beta-sheets leads to a complex phase behavior in which proteins can assemble into various types of aggregates including crystals, liquidlike phases of…
Building better models of cellular pathways is one of the major challenges of systems biology and functional genomics. There is a need for methods to build on established expert knowledge and reconcile it with results of high-throughput…
The relationship between interactions, flexibility and disorder in proteins has been explored from many angles: folding upon binding, flexibility of the core relative to the periphery, entropy changes, etc. In this work, we provide…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
Causal discovery can be a powerful tool for investigating causality when a system can be observed but is inaccessible to experiments in practice. Despite this, it is rarely used in any scientific or medical fields. One of the major hurdles…
This paper investigates given an assembly graph, find the possible micronuclear sequences in terms of MDSs and IESs; which represent Hamiltonian polygonal paths. We will consider the orientations of the assembly graph and Hamiltonian…
Self-assembly of complex and functional materials remains a grand challenge in soft material science. Efficient assembly depends on a delicate balance between thermodynamic and kinetic effects, requiring fine-tuning affinities and…
Addressable self-assembly is the formation of a target structure from a set of unique molecular or colloidal building-blocks, each of which occupies a defined location in the target. The requirement that each type of building-block appears…
The self-assembly of particles into organized structures is a key feature of living organisms and a major engineering challenge. While it may proceed through the binding of perfectly matched, puzzle-pieces-like particles, many other…