Physical Sciences and Mathematics Commons^™

Asymptotic Multi-Layer Analysis Of Wind Over Unsteady Monochromatic Surface Waves, Shahrdad Sajjadi, Julian Hunt, Frederique Drullion

Publications

Asymptotic multi-layer analyses and computation of solutions for turbulent flows over steady and unsteady monochromatic surface wave are reviewed, in the limits of low turbulent stresses and small wave amplitude. The structure of the flow is defined in terms of asymptotically-matched thin-layers, namely the surface layer and a critical layer, whether it is ‘elevated’ or ‘immersed’, corresponding to its location above or within the surface layer. The results particularly demonstrate the physical importance of the singular flow features and physical implications of the elevated critical layer in the limit of the unsteadiness tending to zero. These agree with the variational …

A Study Of Energy Transfer Of Wind And Ocean Waves, Shahrdad Sajjadi, Mason Bray

Publications

To develop a better understanding of energy transfer between wind and different types of waves a model was created to determine growth factors and energy transfers on breaking waves and the resulting velocity vectors. This model was used to build on the research of Sajjadi et al (1996) on the growth of waves by sheared flow and takes models of wave velocities developed by Weber and Melsom (1993) and end energy transfer by Sajjadi, Hunt and Drullion (2012).

Preferential Scattering By Interfacial Charged Defects For Enhanced Thermoelectric Performance In Few-Layered N-Type Bi2te3, Pooja Puneet, Ramakrishna Podila, Mehmet Karakaya, Song Zhu, Jian He, Terry M. Tritt, Mildred S. Dresselhaus, Apparao Rao

Publications

Over the past two decades several nano-structuring methods have helped improve the figure of merit (ZT) in the state-of-the art bulk thermoelectric materials. While these methods could enhance the thermoelectric performance of p-type Bi₂Te₃, it was frustrating to researchers that they proved ineffective for n-type Bi₂Te₃ due to the inevitable deterioration of its thermoelectric properties in the basal plane. Here, we describe a novel chemical-exfoliation spark-plasma-sintering (CE-SPS) nano-structuring process, which transforms the microstructure of n-type Bi₂Te₃ in an extraordinary manner without compromising its basal plane …

Molecular Mechanisms Of Disease-Causing Missense Mutations, Shannon Stefl, Hafumi Nishi, Marharyta Petukh, Anna R. Panchenko, Emil Alexov

Publications

Genetic variations resulting in a change of amino acid sequence can have a dramatic effect on stability, hydrogen bond network, conformational dynamics, activity and many other physiologically important properties of proteins. The substitutions of only one residue in a protein sequence, so-called missense mutations, can be related to many pathological conditions, and may influence susceptibility to disease and drug treatment. The plausible effects of missense mutations range from affecting the macromolecular stability to perturbing macromolecular interactions and cellular localization. Here we review the individual cases and genome-wide studies which illustrate the association between missense mutations and diseases. In addition we …

Optical And Thermal Properties Of Spinel With Revised (Increased) Absorption At 4 To 5 Μm Wavelengths And Comparison With Sapphire, Daniel C. Harris, Giorgio Turri

Publications

Infrared absorption of high-quality, commercial, polycrystalline MgAl2O4 spinel is ∼40% greater in the range of 3.8 to 5.0 μm than the value predicted by the computer code OPTIMATR®, which has been used for window and dome design for more than 20 years. As a result, spinel and a-plane sapphire windows designed to support the same external pressure with the same probability of survival have approximately the same infrared absorptance in the range 3.8 to 5.0 μm. c-Plane sapphire has greater absorptance than spinel in the range 3.8 to 5.0 μm. Spinel has two weak absorption bands near 1.8 and 3.0 …

Continuous Development Of Schemes For Parallel Computing Of The Electrostatics In Biological Systems: Implementation In Delphi, Chuan Li, Marharyta Petukh, Lin Li, Emil Alexov

Publications

Due to the enormous importance of electrostatics in molecular biology, calculating the electrostatic potential and corresponding energies has become a standard computational approach for the study of biomolecules and nano-objects immersed in water and salt phase or other media. However, the electrostatics of large macromolecules and macromolecular complexes, including nano-objects, may not be obtainable via explicit methods and even the standard continuum electrostatics methods may not be applicable due to high computational time and memory requirements. Here, we report further development of the parallelization scheme reported in our previous work (J Comput Chem. 2012 Sep 15; 33(24):1960–6.) to include parallelization …

Cancer Missense Mutations Alter Binding Properties Of Proteins And Their Interaction Networks, Hafumi Nisha, Manoj Tyagi, Shaolei Teng, Benjamin A. Shoemaker, Kosuke Hashimoto, Emil Alexov, Stefan Wuchty, Anna R. Panchenko

Publications

Many studies have shown that missense mutations might play an important role in carcinogenesis. However, the extent to which cancer mutations might affect biomolecular interactions remains unclear. Here, we map glioblastoma missense mutations on the human protein interactome, model the structures of affected protein complexes and decipher the effect of mutations on protein-protein, protein-nucleic acid and protein-ion binding interfaces. Although some missense mutations over-stabilize protein complexes, we found that the overall effect of mutations is destabilizing, mostly affecting the electrostatic component of binding energy. We also showed that mutations on interfaces resulted in more drastic changes of amino acid physico-chemical …

The Role Of Protonation States In Ligand-Receptor Recognition And Binding, Marharyta Petukh, Shannon Stefl, Emil Alexov

Publications

In this review we discuss the role of protonation states in receptor-ligand interactions, providing experimental evidences and computational predictions that complex formation may involve titratable groups with unusual pKa’s and that protonation states frequently change from unbound to bound states. These protonation changes result in proton uptake/release, which in turn causes the pHdependence of the binding. Indeed, experimental data strongly suggest that almost any binding is pH-dependent and to be correctly modeled, the protonation states must be properly assigned prior to and after the binding. One may accurately predict the protonation states when provided with the structures of the unbound …

Nanobiotechnology Can Boost Crop Production And Quality: First Evidence From Increased Plant Biomass, Fruit Yield And Phytomedicine Content In Bitter Melon (Momordica Charantia), Chittaranjan Kole, Phullara Kole, K Manoj Randunu, Poonam Choudhary, Ramakrishna Podila, Pu Chen Ke, Apparao M. Rao, Richard K. Marcus

Publications

BACKGROUND:

Recent research on nanoparticles in a number of crops has evidenced for enhanced germination and seedling growth, physiological activities including photosynthetic activity and nitrogen metabolism, mRNA expression and protein level, and also positive changes in gene expression indicating their potential use in crop improvement. We used a medicinally rich vegetable crop, bitter melon, as a model to evaluate the effects of seed treatment with a carbon-based nanoparticle, fullerol [C60(OH)20], on yield of plant biomass and fruit characters, and phytomedicine contents in fruits.

RESULTS:

We confirmed the uptake, translocation and accumulation of fullerol through bright field imaging and Fourier transform …

Progress In Developing Poisson-Boltzmann Equation Solvers, Chuan Li, Marharyta Petukh, Emil Alexov

Publications

This review outlines the recent progress made in developing more accurate and efficient solutions to model electrostatics in systems comprised of bio-macromolecules and nano-objects, the last one referring to objects that do not have biological function themselves but nowadays are frequently used in biophysical and medical approaches in conjunction with bio-macromolecules. The problem of modeling macromolecular electrostatics is reviewed from two different angles: as a mathematical task provided the specific definition of the system to be modeled and as a physical problem aiming to better capture the phenomena occurring in the real experiments. In addition, specific attention is paid to …

A Rational Free Energy-Based Approach To Understanding And Targeting Disease-Causing Missense Mutations., Zhe Zhang, Shawn Witham, Marharita Petukh, Gautier Moroy, Maria Miteva, Yoshihiko Ikeguchi, Emil Alexov

Publications

BACKGROUND AND SIGNIFICANCE:

Intellectual disability is a condition characterized by significant limitations in cognitive abilities and social/behavioral adaptive skills and is an important reason for pediatric, neurologic, and genetic referrals. Approximately 10% of protein-encoding genes on the X chromosome are implicated in intellectual disability, and the corresponding intellectual disability is termed X-linked ID (XLID). Although few mutations and a small number of families have been identified and XLID is rare, collectively the impact of XLID is significant because patients usually are unable to fully participate in society.

OBJECTIVE:

To reveal the molecular mechanisms of various intellectual disabilities and to suggest …

Enhancing Human Spermine Synthase Activity By Engineered Mutations, Zhe Zhang, Yueli Zheng, Margo Petukh, Anthony Pegg, Yoshihiko Ikeguchi, Emil Alexov

Publications

Spermine synthase (SMS) is an enzyme which function is to convert spermidine into spermine. It was shown that gene defects resulting in amino acid changes of the wild type SMS cause Snyder-Robinson syndrome, which is a mild-to-moderate mental disability associated with osteoporosis, facial asymmetry, thin habitus, hypotonia, and a nonspecific movement disorder. These disease-causing missense mutations were demonstrated, both in silico and in vitro, to affect the wild type function of SMS by either destabilizing the SMS dimer/monomer or directly affecting the hydrogen bond network of the active site of SMS. In contrast to these studies, here we report an …

Delphi Web Server: A Comprehensive Online Suite For Electrostatic Calculations Of Biological Macromolecules And Their Complexes., Subhra Sarkar, Shawn Witham, Jie Zhang, Maxim Zhenirovskyy, Walter Rocchia

Publications

Here we report a web server, the DelPhi web server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric map. The server provides extra services to fix structural defects, as missing atoms in the structural file and allows for generation of missing hydrogen atoms. The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22, Amber98 or OPLS. Upon completion of the calculations, the user is given option to download fixed and protonated structural file, together with the parameter and Delphi output …

Between Algorithm And Model: Different Molecular Surface Definitions For The Poisson-Boltzmann Based Electrostatic Characterization Of Biomolecules In Solution, Sergio Decherchi, José Colmenares, Chiara Eva Catalano, Michela Spagnuolo, Emil Alexov, Walter Rocchia

Publications

The definition of a molecular surface which is physically sound and computationally efficient is a very interesting and long standing problem in the implicit solvent continuum modeling of biomolecular systems as well as in the molecular graphics field. In this work, two molecular surfaces are evaluated with respect to their suitability for electrostatic computation as alternatives to the widely used Connolly-Richards surface: the blobby surface, an implicit Gaussian atom centered surface, and the skin surface. As figures of merit, we considered surface differentiability and surface area continuity with respect to atom positions, and the agreement with explicit solvent simulations. Geometric …

In Silico Investigation Of Ph-Dependence Of Prolactin And Human Growth Hormone Binding To Human Prolactin Receptor, Lin Wang, Shawn Witham, Zhe Zhang, Michael E. Hodsdon, Emil Alexov

Publications

Experimental data shows that the binding of human prolactin (hPRL) to human prolactin receptor (hPRLr-ECD) is strongly pH-dependent, while the binding of the same receptor to human growth hormone (hGH) is pH-independent. Here we carry in silico analysis of the molecular effects causing such a difference and reveal the role of individual amino acids. It is shown that the computational modeling correctly predicts experimentally determined pKa’s of histidine residues in an unbound state in the majority of the cases and the pH-dependence of the binding free energy. Structural analysis carried in conjunction with calculated pH-dependence of the binding revealed that …

Using Delphi Capabilities To Mimic Protein's Conformational Reorganization With Amino Acid Specific Dielectric Constants, Lin Wang, Zhe Zhang, Walter Rocchia, Emil Alexov

Publications

Many molecular events are associated with small or large conformational changes occurring in the corresponding proteins. Modeling such changes is a challenge and requires significant amount of computing time. From point of view of electrostatics, these changes can be viewed as a reorganization of local charges and dipoles in response to the changes of the electrostatic field, if the cause is insertion or deletion of a charged amino acid. Here we report a large scale investigation of modeling the changes of the folding energy due to single mutations involving charged group. This allows the changes of the folding energy to …

Elevated Electron Temperatures Around Twin Sporadic E Layers At Low Latitude: Observations And The Case For A Plausible Link To Currents Parallel To The Geomagnetic Field, Aroh Barjatya, J. P. St. Maurice, C. M. Swenson

Publications

We present data from nighttime sounding rocket flights in the low latitude E region. The payloads carried a sweeping Langmuir probe, a plasma impedance probe, and electric field probes. A detailed examination of the plasma density, temperature, and electric field measurements show two strong sporadic E (Es) layers with very high electron temperatures (∼1000 K) on each side of the upper layer. The lower layer was consistent with the presence of a strong zonal neutral wind shear. The upper layer was strongly influenced by the presence of a strongly negative vertical electric field, with zonal winds and …

Multi-Instrument Comparisons Of D-Region Plasma Measurements, M. Friedrich, K. M. Torkar, U. P. Hoppe, T. A. Bekkeng, Aroh Barjatya, M. Rapp

Publications

The ECOMA (Existence and Charge state Of Meteoric dust grains in the middle Atmosphere) series of sounding rocket flights consisted of nine flights with almost identical payload design and flight characteristics. All flights carried a radio wave propagation experiment together with a variety of plasma probes. Three of these measured electron densities, two ion densities. The rockets were all launched from the Andøya Rocket Range, Norway, in four campaigns between 2006 and 2010. Emphasis is on the final three flights from 2010 where the payloads were equipped with four instruments capable of measuring plasma densities in situ, among them a …

Payload Charging Events In The Mesosphere And Their Impact On Langmuir Type Electric Probes, T. A. Bekkeng, Aroh Barjatya, U. P. Hoppe, M. Friedrich

Publications

Three sounding rockets were launched from Andøya Rocket Range in the ECOMA campaign in December 2010. The aim was to study the evolution of meteoric smoke particles during a major meteor shower. Of the various instruments onboard the rocket payload, this paper presents the data from a multi-Needle Langmuir Probe (m-NLP) and a charged dust detector. The payload floating potential, as observed using the m-NLP instrument, shows charging events on two of the three flights. These charging events cannot be explained using a simple charging model, and have implications towards the use of fixed bias Langmuir probes on sounding rockets …