Related papers: A colloid approach to self-assembling antibodies
Results from molecular dynamics simulations of simple, structured particles capable of self-assembling into polyhedral shells are described. The analysis focuses on the growth histories of individual shells in the presence of an explicit…
We consider a model of dynamics of the immune system. The model is based on three factors: occasional boosting and continuous waning of immunity and a general description of the period between subsequent boosting events. The antibody…
In this paper, we develop a thermodynamic perturbation theory to describe the self-assembly of patchy colloids which exhibit both patch-patch attractions as well as patch / non-patch attractions. That is, patches attract other patches as…
An unsolved challenge in the development of antigen specific immunotherapies is determining the optimal antigens to target. Comprehension of antigen-MHC binding is paramount towards achieving this goal. Here, we present CASTELO, a combined…
Single-stranded RNA viruses co-assemble their capsid with the genome and variations in capsid structures can have significant functional relevance. In particular, viruses need to respond to a dehydrating environment to prevent genomic…
We investigate the structural properties of a simple model for tetrahedral patchy colloids in which the patch width and the patch range can be tuned independently. For wide bond angles, a fully bonded network can be generated by standard…
A simple model of an active colloid consisting of dumbbell-shaped particles that cyclically change their length without propelling themselves is proposed and analyzed. At nanoscales, it represents an idealization for bacterial cytoplasm or…
Image processing and pattern recognition offer a useful and versatile method for optically characterizing drops of a colloidal solution during the drying process and in its final state. This paper exploits image processing techniques…
Active colloids belong to a class of non-equilibrium systems where energy uptake, conversion and dissipation occurs at the level of individual colloidal particles, which can lead to particles self-propelled motion and surprising collective…
We describe the representation of the chemical affinity between the antigen-combining site of the immunoglobulin molecule and the antigen molecule as the probability of the two molecules existing in a bound state. Our model is based on the…
Many problems in materials science and biology involve particles interacting with strong, short-ranged bonds, that can break and form on experimental timescales. Treating such bonds as constraints can significantly speed up sampling their…
One of the fundamental goals of nanotechnology is to exploit selective and directional interactions between molecules to design particles that self-assemble into desired structures, from capsids, to nano-clusters, to fully formed crystals…
Inverse patchy colloids are nano- to micro-scale particles with a surface divided into differently charged regions. This class of colloids combines directional, selective bonding with a relatively simple particle design: owing to the…
The toxins associated with infectious diseases are potential targets for inhibitors which have the potential for prophylactic or therapeutic use. Many antibodies have been generated for this purpose, and the objective of this study was to…
A simple theoretical approach is used to investigate active colloids at the free interface and near repulsive substrates. We employ dynamical density functional theory to determine the steady-state density profiles in an effective…
Antibodies are proteins produced by the immune system that recognize and bind to specific antigens, and their 3D structures are crucial for understanding their binding mechanism and designing therapeutic interventions. The specificity of…
The connection between the properties of cell tissue and those of the single constituent cells remains to be elucidated. At the purely mechanical level, the degree of rigidity of different cellular components, such as the nucleus and the…
In this work we introduce an Autoencoder for molecular conformations. Our proposed model converts the discrete spatial arrangements of atoms in a given molecular graph (conformation) into and from a continuous fixed-sized latent…
We propose a flexible Bayesian approach for estimating the joint density of a multivariate outcome of interest in the presence of categorical covariates. Leveraging a Gaussian copula framework, our method effectively captures the dependence…
Advances in experimental techniques and in theoretical models have improved our understanding of protein crystallization. But they have also left open questions regarding the protein phase behavior and self-assembly kinetics, such as why…