Arman Fathizadeh

Arman Fathizadeh
University of Texas at Austin | UT · Institute for Computational Engineering and Sciences

PhD

About

42
Publications
3,907
Reads
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599
Citations
Citations since 2016
31 Research Items
537 Citations
2016201720182019202020212022020406080100
2016201720182019202020212022020406080100
2016201720182019202020212022020406080100
2016201720182019202020212022020406080100

Publications

Publications (42)
Article
A physical understanding of membrane permeation and translocation by small, positively charged molecules can illuminate cell penetrating peptide mechanisms of entry and inform drug design. We have previously investigated the permeation of the doubly charged peptide WKW and proposed a defect-assisted permeation mechanism where a small molecule with...
Article
Full-text available
Two-dimensional nanosheets, such as the general family of graphenes have attracted considerable attention over the past decade, due to their excellent thermal, mechanical, and electrical properties. We report on the result of a study of separation of gaseous mixtures by a model graphyne-3 membrane, using extensive molecular dynamics simulations and...
Preprint
Full-text available
Two-dimensional nanosheets, such as the general family of graphenes have attracted considerable attention over the past decade, due to their excellent thermal, mechanical, and electrical properties. We report on the result of a study of separation of gaseous mixtures by a model graphyne-3 membrane, using extensive molecular dynamics simulations and...
Article
Phospholipid membranes support essential biochemical processes, yet remain difficult to characterize due to their compositional and structural heterogeneity. The two most common phospholipid headgroup structures in biological membranes are phosphatidylcholine (PC) and phosphatidylethanolamine (PE), but interactions between PC and PE lipids remain u...
Article
Time scales are of paramount importance in biology. Living systems exploit variations in time scales to aim processes in desired directions. The network of biochemical reactions shapes cellular responses and metabolism. Enzymes speed up the rate of reactions and molecular machines carry on cellular tasks. Significant efforts are invested in studyin...
Article
Full-text available
Computational determination of the equilibrium state of heterogeneous phospholipid membranes is a significant challenge. We wish to explore the rich phase diagram of these multi-component systems. However, the diffusion and mixing times in membranes are long compared to typical time scales of computer simulations. Here, we evaluate the combination...
Article
Membranes serve diverse functions in biological systems. Variations in their molecular compositions impact their physical properties and lead to rich phase behavior such as switching from gel to fluid phase and/or separation to micro and macrodomains with different molecular compositions. We present a combined computational and experimental study o...
Preprint
Computational determination of the equilibrium state of heterogeneous phospholipid mem-branes is a significant challenge. We wish to explore the rich phase diagram of these multi-component systems. However, the diffusion and mixing times in membranes are long com-pared to typical times of computer simulations. To speed up the relaxation times, adva...
Chapter
Molecular dynamics (MD) studies of biomolecules require the ability to simulate complex biochemical systems with an increasingly larger number of particles and for longer time scales, a problem that cannot be overcome by computational hardware advances alone. A main problem springs from the intrinsically high-dimensional and complex nature of the u...
Article
Background: Kinases are a family of enzymes that catalyze the transfer of the ɤ-phosphate group from ATP to a protein's residue. Malfunctioning kinases are involved in many health problems such as cardiovascular diseases, diabetes, and cancer. Kinases transitions between multiple conformations of inactive to active forms attracted considerable int...
Article
We investigate membrane permeation by the peptide WKW that is amidated at its C-terminus and therefore carries a positive charge of +2. To facilitate an efficient calculation, we introduce a novel set of simple coarse variables that measure permeation depth and membrane distortion. The phospholipid head groups shift toward the center of the membran...
Article
We investigate the thermodynamics and kinetics of the permeation of a potassium ion through a phospholipid membrane. We illustrate that the conventional reaction coordinate (the position of the ion along the normal to the membrane plane) is insufficient to capture essential elements of the process. It is necessary to add coarse variables that measu...
Article
An algorithm to efficiently simulate multi-component fluids is proposed and illustrated. The focus is on biological membranes that are heterogeneous and challenging to investigate quantitatively. To achieve rapid equilibration of spatially inhomogeneous fluids, we mix conventional molecular dynamics simulations with alchemical trajectories. The alc...
Article
The calculation of minimum energy or minimum free energy paths is an important step in the quantitative and qualitative studies of chemical and physical processes. The computations of these coordinates present a significant challenge and have attracted considerable theoretical and computational interest. Here we present a new local-global approach...
Article
Full-text available
In many device architectures based on 2D materials, a major part of the heat generated in hot-spots dissipates in the through-plane direction where the interfacial thermal resistances can significantly restrain the heat removal capability of the device. Despite its importance, there is an enormous (1–2 orders of magnitude) disagreement in the liter...
Article
Full-text available
Reaction coordinates are vital tools for qualitative and quantitative analysis of molecular processes. They provide a simple picture of reaction progress and essential input for calculations of free energies and rates. Iso-committor surfaces are considered the optimal reaction coordinate. We present an algorithm to compute efficiently a sequence of...
Article
The large-scale conformation of DNA molecules plays a critical role in many basic elements of cellular functionality and viability. By targeting the structural properties of DNA, many cancer drugs, such as anthracyclines, effectively inhibit tumor growth but can also produce dangerous side effects. To enhance the development of innovative medicatio...
Article
Full-text available
The motion of a fullerene (C60) on 5 different types of graphyne is studied by all-atom molecular dynamics simulations and compared with former studies on the motion of C60 on graphene. The motion shows a diffusive behavior which consists of either a continuous motion or discrete movements between trapping sites depending on the type of the graphyn...
Article
Full-text available
Graphene has served as the model 2D system for over a decade, and the effects of grain boundaries (GBs) on its electrical and mechanical properties are very well investigated. However, no direct measurement of the correlation between thermal transport and graphene GBs has been reported. Here, we report a simultaneous comparison of thermal transport...
Article
Over the course of its life cycle, a cell's DNA undergoes many carefully orchestrated topological changes, which facilitate vital cellular processes such as replication and transcription. Consequently, unresolved conformational defects in the structure can interfere with critical interactions, and may result in genetic anomalies that culminate in c...
Article
Gram Negative Bacteria such as E. Coli use a tripartite complex system to expel toxic chemicals, such as antibiotics, and ions out of the cell. In E.Coli, CusCBA, which is a complex of an inner membrane transporter (CusA), a connecting fusion protein (CusB), and an outer membrane channel (CusC), utilizes the proton motive force to transport copper...
Article
DNA supercoiling is a widespread phenomenon in biology. Here we introduce a coarse-grained DNA model and study supercoiled DNA rings via a rigid body molecular dynamics simulation. Our model allows us to investigate these structures in more detail than previously. The simulations are performed on rings of one to six kilobase pairs length and are co...
Article
It is well recognized that the primary interaction of most biological environments with nanoparticles (NPs) is strongly influenced by a long-lived ("hard") protein corona that surrounds the NP and remains strongly adsorbed to its surface. The amount and composition of associated proteins in the corona adsorbed onto the NPs is related to several imp...
Article
Full-text available
We study the conformations of a semiflexible chain, confined in nano-scaled spherical cavities, under two distinct processes of confinement. Radial contraction and packaging are employed as two confining procedures. The former method is performed by gradually decreasing the diameter of a spherical shell which envelopes a confined chain. The latter...
Article
Full-text available
The majority of eukaryotic DNA, about three quarter, is wrapped around histone proteins forming so-called nucleosomes. To study nucleosomal DNA we introduce a coarse-grained molecular dynamics model based on sequence-dependent harmonic rigid base pair step parameters of DNA and nucleosomal binding sites. Mixed parametrization based on all-atom mole...
Article
By considering the detailed structure of DNA in the base pair level, two possible definitions of the persistence length are compared. One definition is related to the orientation of the terminal base pairs, and the other is based on the vectors which connect two adjacent base pairs at each end of the molecule. It is shown that although these defini...
Conference Paper
In this paper a semi-analytical method is developed to analyze functionally graded cylindrical panels. In this method, the radial domain is divided into some finite sub-domains and the material properties are assumed to be constant in each subdomain. Imposing the continuity conditions at the interface of the adjacent sub-domains, together with the...

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