14 citations · 37 across the 10 of their papers we have counts for
13 papers
Aggregation and structural phase transitions of semiflexible polymer bundles: a braided circuit topology approach
Jonas Berx, Alireza Mashaghi
We present a braided circuit topology framework for investigating topology and structural phase transitions in aggregates of semiflexible polymers. In the conventional approach to…
Decoding chirality in circuit topology of a self entangled chain through braiding
Jonas Berx, Alireza Mashaghi
Circuit topology employs fundamental units of entanglement, known as soft contacts, for constructing knots from the bottom up, utilising circuit topology relations, namely parallel…
Polynomial Invariant of Molecular Circuit Topology
Alireza Mashaghi, Roland van der Veen
The topological framework of circuit topology has recently been introduced to complement knot theory and to help in understanding the physics of molecular folding. Naturally evolve…
Circuit topology for bottom-up engineering of molecular knots
Anatoly Golovnev, Alireza Mashaghi
The art of tying knots is exploited in nature and occurs in multiple applications ranging from being an essential part of scouting programs to engineering molecular knots. Biomolec…
Enhancement of the Coloring Invariant for Folded Molecular Chains
Jose Ceniceros, Mohamed Elhamdadi, Alireza Mashaghi
Folded linear molecular chains are ubiquitous in biology. Folding is mediated by intra-chain interactions that "glue" two or more regions of a chain. The resulting fold topology is…
Knot Theory for Proteins: Gauss Codes, Quandles and Bondles
Colin Adams, Judah Devadoss, Mohamed Elhamdadi +1
Proteins are linear molecular chains that often fold to function. The topology of folding is widely believed to define its properties and function, and knot theory has been applied…
Statistical Physics of Medical Diagnostics: Study of a Probabilistic Model
Alireza Mashaghi, Abolfazl Ramezanpour
We study a diagnostic strategy which is based on the anticipation of the diagnostic process by simulation of the dynamical process starting from the initial findings. We show that…
Search efficiency of biased migration towards stationary or moving targets in heterogeneously structured environments
Youness Azimzade, Alireza Mashaghi
Efficient search acts as a strong selective force in biological systems ranging from cellular populations to predator-prey systems. The search processes commonly involve finding a…
State assignment problem in systems biology and medicine: on the importance of state interaction network topology
Abolfazl Ramezanpour, Alireza Mashaghi
A fundamental problem in medicine and biology is to assign states, e.g. healthy or diseased, to cells, organs or individuals. State assignment or making a diagnosis is often a nont…
Topology Sorting and Characterization of Folded Polymers Using Nano-pores
Narges Nikoofard, Alireza Mashaghi
Here we report on the translocation of folded polymers through nano-pores using molecular dynamic simulations. Two cases are studied; one in which a folded molecule unfolds upon pa…
Distance measures and evolution of polymer chains in their topological space
Alireza Mashaghi, Abolfazl Ramezanpour
Conformational transitions are ubiquitous in biomolecular systems, have significant functional roles and are subject to evolutionary pressures. Here we provide a first theoretical…
Circuit topology of linear polymers: a statistical mechanical treatment
Alireza Mashaghi, Abolfazl Ramezanpour
Circuit topology refers to the arrangement of interactions between objects belonging to a linearly ordered object set. Linearly ordered set of objects are common in nature and occu…
A physicist's view of DNA
Alireza Mashaghi, Allard Katan
Nucleic acids, like DNA and RNA, are molecules that are present in any life form. Their most notable function is to encode biological information. Why then would a physicist be int…