Mitchell, Saige M Pajovich, Harrison T Broas, Sarah M Hugo, Mindy M Banerjee, Ipsita A
Published in
Journal of biomolecular structure & dynamics
Tissue engineering (TE) aims to repair and regenerate damaged tissue by an assimilation of optimal combination of cells specific to the tissue with an appropriate biomaterial. In this work, a new biomaterial for potential cardiac TE applications was developed by utilizing a combination of in silico studies and in vitro experiments. Molecular dynami...
Coronel, M B Marzola Fraenza, C C Anoardo, E
Published in
Chemistry and physics of lipids
Liposomes with enhanced elasticity have been proven to increase the efficiency of drug transport across the skin. The understanding of the background physicochemical processes driving the liposome viscoelastic properties is an essential feature for the design of effective formulations involving different lipids and additive molecules. In this work ...
Liu, Guohong Yan, Xiliang Li, Chengjun Hu, Song Yan, Jiachen Yan, Bing
Published in
Journal of hazardous materials
The environmental fate of transition-metal dichalcogenides (TMDCs) may be further complicated by interacting with existing pollutants, especially per- and polyfluoroalkyl substances (PFAS). However, due to their sheer volume, it is impossible to explore all possible interactions by simply utilizing experimental methods. Herein, we used two model TM...
Ji, Joonho Lee, Byeong-Joo
© 2022 Elsevier B.V.LiNixMnyCozO2 (x + y + z = 1, x > 0.6) Ni-rich layered structures are the most investigated and used cathode materials these days due to their high energy density. However, it is hard to avoid Li/Ni intermixing during synthesis and the charge/discharge cycle. This intermixing is known to degrade the cathode by inducing anisotrop...
Kim, Seon Beom Farrag, Marwa Mishra, Sushil K Misra, Sandeep K Sharp, Joshua S Doerksen, Robert J Pomin, Vitor H
Published in
Carbohydrate polymers
Sulfated fucans (SFs) from echinoderms, such as sea cucumbers and sea urchins, present linear and regular sulfation patterns within defined oligosaccharide building blocks. The high molecular weights of these polymers pose a problem in advanced structure-activity relationship studies for which derived oligosaccharides are more appropriate tools for...
Liu, Jun Chen, Changzhou Tu, Wenfeng Liu, Wei Zhang, Yanru
Published in
Journal of molecular graphics & modelling
The dissolution and microscopic interactions of processed Polygonatum cyrtonema polysaccharides in water are extremely important because they strongly influence the process to extract these polysaccharides from water. In this paper, molecular dynamics simulation methods were used to analyse the influence of extraction temperature, concentration and...
Capelli, Riccardo Serapian, Stefano A Colombo, Giorgio
Published in
Methods in molecular biology (Clifton, N.J.)
The design of optimized protein antigens is a fundamental step in the development of new vaccine candidates and in the detection of therapeutic antibodies. A fundamental prerequisite is the identification of antigenic regions that are most prone to interact with antibodies, namely, B-cell epitopes. Here, we describe an efficient structure-based com...
Neamtu, Andrei Mocci, Francesca Laaksonen, Aatto Barroso da Silva, Fernando L
Published in
Colloids and surfaces. B, Biointerfaces
A highly efficient and robust multiple scales in silico protocol, consisting of atomistic Molecular Dynamics (MD), coarse-grain (CG) MD, and constant-pH CG Monte Carlo (MC), has been developed and used to study the binding affinities of selected antigen-binding fragments of the monoclonal antibody (mAbs) CR3022 and several of its here optimized ver...
Jia, Lei Sun, Yaxiong
Published in
Methods in molecular biology (Clifton, N.J.)
In silico prediction methods were developed to predict protein asparagine (Asn) deamidation. The method is based on understanding deamidation mechanism on structural level with machine learning. Our structure-based method is more accurate than the sequence-based method which is still widely used in protein engineering process. In addition, molecula...
Harris, B Liu, GY Faller, R
This work presents a novel general tool for modeling the process of evaporation without the need for modifying existing software using Python. The tool was developed based on the MDAnalysis package, which is used to import a Molecular Dynamics trajectory. The tool then removes solvent molecules and outputs a new structure file to be used for furthe...
