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Cell-penetrating peptides (CPPs) are powerful vectors for the intracellular delivery of a diverse array of therapeutic molecules. Despite their potential, the rational design of CPPs remains a challenging task that often requires extensive…

Identification of antimicrobial peptides is an important and necessary issue in today's era. Antimicrobial peptides are essential as an alternative to antibiotics for biomedical applications and many other practical applications. These…

Antimicrobial peptides have emerged as promising molecules to combat antimicrobial resistance. However, fragmented datasets, inconsistent annotations, and the lack of standardized benchmarks hinder computational approaches and slow down the…

Membrane proteins often need to be inserted into or attached on the cell membrane to perform their functions. Understanding their transmembrane topology and conformational dynamics during insertion is crucial for elucidating their roles.…

We develop theory and computational methods to investigate particle inclusions embedded within curved lipid bilayer membranes. We consider the case of spherical lipid vesicles where inclusion particles are coupled through (i) intramembrane…

Both molecular mechanical and quantum mechanical calculations play an important role in describing the behavior and structure of molecules. In this work, we compare for the same peptide systems the results obtained from folding molecular…

As the development of new classes of antibiotics slows, bacterial resistance to existing antibiotics is becoming an increasing problem. A potential solution is to develop treatment strategies with an alternative mode of action. We consider…

Antimicrobial protocols - using substances such as antibiotics or disinfectants - remain the preferred option for preventing the spread of pathogenic bacteria. However, bacteria can develop mechanisms to reduce their antimicrobial…

We study the aggregation of peptides using the discrete molecular dynamics simulations. At temperatures above the alpha-helix melting temperature of a single peptide, the model peptides aggregate into a multi-layer parallel beta-sheet…

In this paper, we propose applying semantic embedding to learn the range of behaviors exhibited by molecular swarms, thereby providing a richer set of features to optimize such systems. Specifically, we consider a standard molecular swarm…

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…

Viroporins are small viral proteins that oligomerize in the membrane of host cells and induce the formation of hydrophilic pores in these membranes, thus altering the physiological properties of the host cells. Due to their significance for…

Abeta is a disordered peptide central to Alzheimer's Disease. Aggregation of Abeta has been widely explored, but its molecular crowding less so. The synaptic cleft where Abeta locates only holds 60-70 water molecules along its width. We…

The dynamic interplay between collective cell movement and the various molecules involved in the accompanying cell signalling mechanisms plays a crucial role in many biological processes including normal tissue development and pathological…

Motivated by the biologically important and complex phenomena of A\beta\ peptide aggregation in Alzheimer's disease, we introduce a model and simulation methodology for studying protein aggregation that includes extra-cellular aggregation,…

A major part of membrane function is conducted by proteins, both integral and peripheral. Peripheral membrane proteins temporarily adhere to biological membranes, either to the lipid bilayer or to integral membrane proteins with…

We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…

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…

Often the development of novel functional peptides is not amenable to high throughput or purely computational screening methods. Peptides must be synthesized one at a time in a process that does not generate large amounts of data. One way…

Lipid membranes, the barrier defining living cells and many of their sub-compartments, bind to a wide variety of nano- and micro-meter sized objects. In the presence of strong adhesive forces, membranes can strongly deform and wrap the…