Research
Interests
Ras B. Pandey
“The whole of science is nothing more
than a refinement of everyday thinking. It is for this reason that the critical
thinking of the physicist cannot possibly be restricted to the examination of
concepts in his own specific field. He cannot proceed without considering
critically a much more difficult problem, the problem of analyzing the nature
of everyday thinking.” - Albert Einstein
Over
the years, our research interests are expanded in a number of areas (based on
opportunities and resources at the time), some with overlapping issues.
Problems are briefly described with relevant publications in the following.
Primary goal is to understand the
assembly of materials (bio-inspired, hybrid, complex fluid) from dynamics of such
basic elements as particles, chains, sheets, and blobs and identify their
multi-scale (local-to-global) characteristics. Larger constituents (e.g.,
chains, sheets, aggregates, and micro-gels) can be designed from small units
such as particles. The inter-play between interaction and entropic constraints
of intra- and inter-particle constituents and temperature leads to a range of
structures (self-organized or kinetically assembled) with multi-scale dynamics
(segmental movements to global transport) in complex fluid, biomimetic, and
hybrid materials.
o Biomimetic: Conformation and dynamics of protein and
tethered membranes: the structural relaxation and pathways to stabilities and
multi-scale mode dynamics. Residues mobility, energy, and correlations profiles
of peptides.
o Chain polymer: Polymer chains in solvent, porous media, complex
fluid, and on surfaces. Driven flow response. DNA electrophoresis.
o Branched polymer: Kinetic gelation, Sol-Gel phase transition,
micro-emulsion and lipids, percolation, and aggregation.
o Multi-component materials: Nano-clay-polymer composites,
biofunctionalized nano-structured materials (involving peptide attached gold,
palladium, and montmorillonite clay platelets).
o Surfaces, interfaces, and roughness: Surface, roughness and
interfacial dynamics in thin film growth with a range of constituents
(particles, polymer chains, solvents)
o Driven transport and flow: Flow through porous
media, Self-organizing structure and flow
multi-component complex systems.
o Immune response: Population dynamics of cells.
o Econophysics: Theoretical modeling of stock fluctuations.
o Critical phenomena: Thermal
and geometrical phase transition.
METHODS (and tools used and/or
exposed)
Standard
methods:
Monte Carlo, Direct simulation, Molecular Dynamics, Stochastic simulations,
Lattice Gas. Hybrid methods: involving
a combination of direct, thermodynamic, kinetic, and lattice gasetc. Multi-scale computing: accelerated
simulation (large-scale annealing/stirring) on a discrete lattice followed by
off-lattice (continuum) simulations (nano, micro, macro scales). Analytical theories: Mean field,
many-body, scaling, and renormalization group (RG) methods used in early work. Languages: Fortran, C, C++. Visualization: OpenGL, Povray.
Graphics: XMGrace, GNUplot. Operating systems: Linux, window.
1. Biomimetics
A complete understanding of the structural
stability, and mobility of proteins, lipid and tethered membranes, a diverse
range of cells and their components, and their complex mixture from atomistic
scale to laboratory observables is highly desirable but computationally not
feasible. Even with simplified covalent (peptide bonds) and non-covalent
interactions between side chains of amino acids (charged, polar, and
hydrophobic) with in-vitro or in-vivo environment, investigation of the
energy and structural landscape of protein is too complex to undertake.
Therefore, developing simplified computer simulation models involving effective
media, phenomenological interactions, and steric constraints is almost
un-avoidable. The structural stability
and segmental dynamics of proteins, membranes, and some aspects of cells are
then investigated by efficient algorithms. More realistic interactions, specificity
(e.g., type, size, and sequence) of residues in proteins, chemical and steric
constraints of membranes, pertinent surface characteristics (e.g., markers and
affinity) of cells are continued to be considered systematically step-by-step.
Our primary goals are to substantiate current findings and identify new laws
(global and specific) for structures (shape, size, relaxation, metastability,
and equilibrium), segmental mobility, and global dynamics that will help better
understanding of the biomimetics constituents.
1(a) Protein: We study the structural
relaxation and pathways to stabilities i.e., the rate of approach to native
structures and segmental dynamics with appropriate interactions for polypeptide
residues in solvents and identify the types of structure and dynamics (i.e.,
diffusive, drift, anomalous, etc.). Evaluating the effects of sequencing
(types, numbers, and order of amino acid groups) on the structures (relaxation,
shape, and size) and mobility of protein is the next step. On-going study
includes structural, energy, and mobility profiles of HIV-I protease (1DIFA).
1(b) Membrane: We investigate the
structure and dynamics of tethered membranes, explore the effects of the
quality of solvents, molecular weight, and temperature, and identify general
trends (scaling and empirical).
1(c) Multi-components: Using cell involving
surfaces with specific markers and affinity, we would like to address how
proteins conform onto the surface, how local structures in different sections
of the proteins compare, how segments and global protein relax and move from
the cell surface into the bulk interior. The main goal is to identify the
fundamental laws (universal and detail-specific) that can improve our
understanding of proteomics and biomimetics in order to accelerate the
knowledge revolution in bio-tech (i.e., learning the root causes of diseases,
discovery of new drugs, and bio-materials). On-going investigations include
adsorption-de-sorption of short peptides (A3, Flg, Pd2, Pd4, CR3-1, S2) on
gold, palladium, and clay surfaces.
Related publications:
o
Relaxation
to native conformation of a bond-fluctuating protein chain with hydrophobic and
polar nodes, Johan Bjursell and R.B. Pandey, Phys. Rev. E 70, 052904 (2004).
o
Effects
of temperature and solvent on the structure and transport of a tethered
membrane: Monte Carlo simulation, R.B. Pandey, K.L. Anderson, and B.L. Farmer, J. Polymer Sci. Part B: Polymer Physics 43,
3478 (2005).
o
Multi-scale
mode dynamics of a tethered membrane, R.B. Pandey, K.L. Anderson, and B.L.
Farmer, Phys. Rev. E 75, 061913 (2007).
o
Conformation of a coarse-grained protein
chain (an aspartic acid protease) model in effective solvent by a
bond-fluctuating Monte Carlo simulation, R.B. Pandey and B.L. Farmer, Phys. Rev. E 77, 031902 (2008).
o Residues energy and mobility in-sequence to global structure and dynamics of a HIV-1 protease (1DIFA) by a coarse-grained Monte Carlo simulation, R.B. Pandey and B.L. Farmer, J. Chem. Phys. 130, 044906 (2009).
o Adsorption
of peptides (A3, Flg, Pd2, Pd4) on gold and palladium surfaces by a
coarse-grained
2. Chain Polymer
2 (a) Conformation and
Dynamics:
Short and long time dynamics of polymer chains with coarse-grained models are
studied using lattice and off-lattice simulations in dilute solution to melt,
porous media, gel, and complex polydispersed (multi-component) systems.
Identification of parameter space where standard dynamics (i.e., Rouse,
reptation, post-reptation, diffusion) are valid and prediction of unusual
(anomalous) transport, are important part of our studies along with the
conformational behaviors and related crossovers (expanded, collapsed, elongated
states). We find that the effects of temperature and external field lead to
non-universal conformational and dynamical behaviors, some of which can be
described by empirical relations. Refining and developing these models further
to better understand and predict the fundamental properties of more realistic
systems are our goals.
2 (b) Flow: We address how the
transport properties of a polymer system depend on the magnitude of field,
porosity, and the nature of chains (polyelectrolytes, amphophiles, etc.) as they are driven through
a porous medium such as gel. Complex fluid (a polydispersed system) consists of
chains, branched macromolecules, and particulates of various mass and size
distributions. Range and type of interactions among the solute and solvent
constituents play an important role in controlling their motion. Global
transport of molecules and collective flow lead to viscoelastic properties
(i.e., flow rates, permeability). Computer simulations are designed to
understand effects of these parameters step by step. We observe interesting
nonlinear response properties (i.e., flow rate, radius of gyration, molecular
distribution, etc.) as a function of external field and porosity in
mono-disperse systems - a major finding that cannot be explained by traditional
theories. Carrying out these studies further with more realistic models is one
of our on-going efforts.
2 (c) DNA Electrophoresis: Conformation and
dynamics of biomacromolecules (idealized chains for protein, DNA, and RNA
molecules) in a range of bio-matrices and solvents are of considerable
interest. A number of issues emerge as the chain macromolecules are driven by
electric field in gel electrophoresis: how fast molecules move, how they
conform at the gel boundary and in pores, how the mobility and conformation
depend on the molecular weight (size of the molecules), magnitude of the field,
porosity of the matrix, temperature and the quality of the solvent. While the
transport of molecules through gel with pores larger than the radius of
gyration of the molecules is well known (widely used to identify the conformational
details including sequencing), the problem becomes very difficult when the
molecular size compare with the pore size. Molecular transport and conformation
respond nonlinearly to field in such complex matrix. Further, as the
macromolecules begin to deposit at the pore boundaries due to competition
between the pore barrier and the field, a density profile evolves and an
interface develops. How such interface develops as a function of field,
temperature, and molecular weight are crucial in understanding the errors in
DNA finger printing and designing of bio-inspired materials. A biomimetic issue
such as how the ions transport affects the formation of ion channels via
embedded proteins in internal and external cellular activities.
Related Publications:
o
Driven
chain macromolecule in a heterogeneous membrane-like medium, R.B. Pandey and R.
Seyfarth, Structural Chem. 14, 445 (2003).
o
Polymer
interface changes in electrophoretic deposition, R.B. Pandey, Prog. Organic Coatings, 47, 324 (2003).
o
Density
and conformation with relaxed substrate, bulk, and interface in electrophoretic
deposition of polymer chains, Frank W. Bentrem, Jun Xie, and R. B. Pandey, J. Mol. Structure: THEOCHEM 592, 95 (2002).
o
Interface
relaxation in electrophoretic deposition of polymer chains: Effects of
segmental dynamics, molecular weight, and field, Frank W. Bentrem, Jun Xie, and
R.B. Pandey, Phys. Rev. E 65, 041606
(2002).
o
Electrophoretic
deposition of polymer chains: A Monte Carlo study of density profile and
conformation, G.M. Foo and R.B. Pandey, Biomacromolecules
1, 407 (2000).
o
Effect
of polymer matrix density on molecular segregation and orientational ordering
by a hybrid computer simulation, G.M. Foo and R.B. Pandey, Physica A 282, 375 (2000).
o
Driven
flow and pinning of molecular aggregates in a heterogeneous medium, G.M. Foo
and R.B. Pandey, J. Chem. Phys. 112,
10659 (2000).
o
Electrophoretic
deposition of polymer chains on adsorbing surface in (2+1)-dimensions:
conformational anisotropy and nonuniversal coverage, G.M. Foo andR.B. Pandey, Phys. Rev. Lett. 80, 3767 (1998).
o
Nonuniversal
scaling and conformational crossover of polymer chains in an electrophoretic
deposition, G.M. Foo and R.B. Pandey, Phys.
Rev. Lett. 79, 2903 (1997).
3. Branched Polymer
3 (a) Stochastic growth (Percolation, Aggregation): Percolation phase transitions and
models for reversible and irreversible growth are of immense interest for over
a decade. We focus on understanding the dependence of universality of the phase
transitions and the ramification (and the fractal nature) of the clusters on
the growth process. We have applied the percolation mechanism to understand the
porous structure formed in sedimentation and investigated their transport
properties. We have examined the basic quantities such as "jamming
coverage" (on surfaces) and "jamming volume fraction and
porosity" in such percolation processes with objects of various shapes and
sizes, such as rods and polymer chains. Power laws are predicted for the
dependence of the percolation threshold and jamming coverage on the size of the
chains. Investigation of polydisperse percolating system is one of our future
objectives.
3 (b) Sol-to-gel modeling: In order to understand
the kinetics of gel formation and the nature of sol-to-gel phase transition
beyond the classical theories (Flory-Stockmayer) and percolation models,
solvent and solute mixture are described by appropriate monomers with specific
functional groups. Rate of reaction, mobility of monomers and micro-gel
particles, and degree of reversibility must be incorporated. We have reported
several interesting findings, such as monotonic decay of the gel point on
increasing the mobility, change in universality with the quality of solvent
(good-to-poor), degree of reversibility, and the onset of inhomogeneity.
Interesting gel-to-sol (melting) thermal transition is observed in
thermo-reversible systems where covalent bonds break due to thermal segmental
movements. Extending these modeling to multicomponent systems in order to
design gel with specific rigidity, volume fraction, and other physical
properties with more realistic kinetics would be a natural extension.
3 (c) Micro-emulsions, lipids
and other self-assembled systems: Structural properties of such multi-component
immiscible systems involve molecular units, such as amphophiles, oil, water,
etc. The interaction among the constituents, their conformation and size, and
the temperature govern the evolution of the overall structures. Using lattice
models, we have predicted the formation of various phases (i.e., immiscible
phases separated by a bi-continuous phase). Characterizing the onset of phase
separation, mixing, shape and size of assembled clusters (micelles and lipid
cells to tubules), and their growth rate are some of the fundamental issues we
would like to pursue.
Related publications:
o
Radical
initiated polymerization in a bifunctional mixture via computer simulation,Keri
L. Diamond, R.B. Pandey, and Shelby F. Thames, J. Chem. Phys. 120, 11905 (2004).
o
Simulations
of Sol-to-Gel modeling: effects of mobility, reversibility, and quality of
solvent, R.B. Pandey and Y. Liu, J.
Sol-Gel Sci. Tech.15, 147 (1999).
o
Computer-simulation
studies of kinetic gelation, Y. Liu and
R.B. Pandey, Phys. Rev. B55, 8257 (1997).
o
Inhomogeneity
in gelation and nonuniversality of Sol-to-Gel transition by a computer
simulation model, Y. Liu and R.B.Pandey, Phys.
Rev. E 54, 6609 (1996).
o
Sol-gel
transitions in thermoreversible gels: Onset of gelation and melting, Y. Liu and
R.B. Pandey, J. Chem. Phys. 105, 825
(1996).
o
Lateral
diffusion in a binary lipid system by a computer simulation, R.B. Pandey, Physica A 223, 309 (1996).
o
Micelle
formation, relaxation time, and three-phase coexistence in a microemulsion
model, D. Stauffer, N. Jan, Y. He, R.B. Pandey, D. Gerrard Marangoni and T.
Smith-Palmer, J. Chem. Phys. 100, 6934
(1994).
4. Multi-component
materials
4 (a) Nanocomposites: Vapor deposition,
tapping, thermal annealing, quenching, sintering, and squeeze casting are some
of the common methods used to design custom-tailored composites with desired
mechanical, thermal, and electrical properties. Most of these physical
properties depend not only on the constituents of the mixture, such as the type
of particles, their size and shapes, but also on their distribution and the
fashion in which they are bonded/welded in the sample. We have attempted to
incorporate some of these factors in our evolving models. In our polymer
deposition studies, we have analyzed how the polymer density at the substrate,
interface, and in the bulk depend on molecular weight, temperature, and field
and found many interesting results. Enormous details need to be incorporated to
make these models more realistic in order to gain insight into the physical
properties of specific composite materials. For example, in a clay-polymer nano-composite,
we find that the conformation of clay platelets remain intact unless their
surfaces are modified and the quality of solvent chosen appropriately. We would
like to carry out these studies with applications ranging from industrial
materials in coating and bio-materials to marine geo-materials involving
sediments and clay.
4 (b) Biofunctionalized nano-structured materials: Designing advanced materials from functionalized nano-particles with specific properties has been the subject of intense interest in recent years primarily due to their high potential for critical applications (e.g., energy storage, computer chips, high tech wears and gears). With the current technical advances, surface of appropriate nano-particles can be modified with a relative ease to tailor their characteristics in order to assemble them in a desired morphology for optimal performance. Because of their higher order structures and response, peptides, proteins, and nucleic acids are prime constituents to functionalize nanopatricles, higher order constituents of the nano-structured materials. Peptides are excellent candidate to attach to the surface of a nano-particle to achieve specific characteristics. Peptides possess unique recognition motif with well-defined structures controlled by unique sequence of underlying residues. Interactions between peptides on exposed surfaces and constituents of the multi-component hybrid materials can be modulated by selecting specific solvent. Of particular interest are the bio-functionalized gold and palladium nano-particles for a range of applications such as sensing, catalysis, bio-transport, and bio-recognition. Understanding of dynamics and structural stability of appropriate peptides on gold and palladium surfaces is therefore highly desirable. On-going studies include residue mobility, energy, targeted binding, and structural profiling of a number of short peptides on gold, palladium, and clay surfaces.
Related publications:
o Adsorption of peptides (A3, Flg, Pd2, Pd4) on gold and palladium surfaces by a coarse-grained Monte Carlo simulation, R.B. Pandey, H. Heinz, J. Feng, B.L. Farmer, J.M. Slocik, L.F. Drummy, and R.R. Naik, Phys. Chem. Chem. Phys. (2009).
o
Exfoliation
of a stack of platelets and intercalation of polymer chains: effects of
molecular weight, entanglement, and interaction with the polymer matrix, R.B.
Pandey and B.L. Farmer, J. Poly. Sci. Part B, Polymer Physics 46, 2696 (2008).
o
Sheets:
Entropy dissipation, multi-scale dynamics, dispersion, and intercalation, R.B. Pandey, K.L. Anderson, and B.L. Farmer, Comp. Sci. Engg.
10, 90 (2008).
o
Effect
of temperature and solvent on dispersion of layered platelets by
o
Exfoliation
of stacked sheets: Effects of temperature, platelet size, and quality of
solvent by a
o
Multi-scale
dynamics of an interacting sheet by a Bond-Fluctuating Monte Carlo simulation,
R.B. Pandey, Kelly L. Anderson, B.L. Farmer, J. Poly. Sci. Part B, Polymer Physics 44, 2512 (2006).
5. Surfaces, interfaces,
and roughness
Surface, roughness and interfacial dynamics in
thin film growth with a range of constituents (multi-component particles,
polymer chains, etc.) are studied by coarse-grained computer simulation models.
We address how the surface grows and interface evolves in various deposition
and kinetic processes involving particles of different shapes and sizes,
including chain polymers. We have studied the motion of the front and the
interfacial growth in an immiscible fluid model and predicted the power-law for
the spreading of front and non-universal scaling for the evolution of its fluctuations
(the interface width) - a new interfacial dynamics. Understanding the scaling
laws of the interface width and roughness with parameters, such as size,
driving field, and the nature of the substrates, have been our major focus. We
have also studied the deposition of polymer chains on adsorbing substrates and
observed several interesting phenomena such as onset of oscillations in the
polymer density profiles (a signature of layering), conformational crossover,
and adsorption-desorption transition. Relaxation of the interface width in
polymer deposition is examined in detail. Interesting dependence of relaxed
interface width on the field (power-law decay), molecular weight, and
temperature (non-monotonic) are observed. Vigorous efforts are made in recent
years to understand the film growth in a multi-component system consisting of hydrophobic
and polar groups in aqueous solution, collaboration with experiments on
polyurethane. A more complex system involving fluorinated heterogeneous
colloids with surface markers is underway.
Related publications:
o
Monte
Carlo simulation of a film growth with reactive hydrophobic, polar, and aqueous
components by a covalent bond-fluctuating model, S. Yang and R.B. Pandey, J. Chem. Phys. 126, 174708 (2007).
o
Film
Growth and Surface Roughness with Effective Fluctuating Covalent Bonds in
Evaporating Aqueous Solution of Reactive Hydrophobic and Polar Groups: A
Computer Simulation Model, Shihai Yang, Adam Seyfarth, Sam Bateman, and R. B.
Pandey, Macromol. Theory Simul. 15, 263
(2006).
o
Film
formation from aqueous polyurethane dispersions of reactive hydrophobic and
hydrophilic components: spectroscopic studies and Monte Carlo simulations, D.B.
Otts, Luis A. Cueva-Parra, R.B. Pandey, and M.W. Urban, Langmuir 21, 4034 (2005).
o
Thermal
roughening and deroughening at polymer interfaces in electrophoretic
deposition, Frank W. Bentrem and R.B. Pandey, Macromolecules 38, 992 (2005).
o
Electrophoretic
deposition of polymer chains on adsorbing surface in (2+1)-dimensions:
conformational anisotropy and nonuniversal coverage, G.M. Foo andR.B. Pandey, Phys. Rev. Lett. 80, 3767 (1998).
o
Conformation
and dynamics of polymer chains on dirty surfaces: a discrete-to-continuum
approach, G.M. Foo and R.B. Pandey, J.
Chem. Phys. 109, 1162 (1998).
o
Electro-deposition
of polymer chains on an adsorbing wall: Density profiles and wall coverage,
G.M. Foo and R.B. Pandey, J. Chem. Phys.
107, 10260 (1997).
o
Nonuniversal
scaling and conformational crossover of polymer chains in an electrophoretic
deposition, G.M. Foo and R.B. Pandey, Phys.
Rev. Lett. 79, 2903 (1997).
o
Kinetics
and jamming coverage in a random sequential adsorption of polymer chains, J.-S.
Wang and R.B. Pandey, Phys. Rev. Lett.77,
1773 (1996).
6. Driven transport (Self-organizing structure and flow)
Understanding the transport of interacting
particles (lattice gas, Lennard-Jones, screened Coulomb systems) in
heterogeneous systems has been one of our major interests for many years. We
have predicted fundamental laws for the non-diffusive transport, non-Newtonian
flow, onset of special spatial ordering/pattern, and related commensurate
(order-disorder) transitions as a function of concentration, range of
interaction, temperature, and external fields.
Using the particulate methods, we are able to understand the complex
fluid flow through porous media, a complement to traditional hydrodynamic
approaches. With a hybrid method, we have shown how a complex hydrodynamic
phenomenon such as shock propagates through a clay-like deformable porous
medium. Flow and patterns in
multi-component, miscible and immiscible driven systems are studied as a
function of hydrostatic pressure, temperature, miscibility gaps, porosity, etc.
Interesting results are observed in our on-going efforts to understand the
formation of methane hydrate, dissociation of methane, and its distribution.
Related publications:
o
Can a difference in molecular weights cause
an eruption in a driven flow of self-organizing immiscible system? R.B. Pandey
and J.F. Gettrust, Eur. Phys. J. B 61, 83
(2008).
o
Flow
through a laboratory sediment sample by computer simulation modeling, R.B.
Pandey, A.H. Reed, E. Braithwaite, R. Seyfarth, and J.F. Gettrust, Physica A 374, 501 (2007).
o
Eruptive
Flow Response in a Multi-Component Driven System by an Interacting Lattice Gas
Simulation, R.B. Pandey and J.F. Gettrust, Physica
A 368, 416 (2006).
o
Flow
Response of a Segregating Mixture by Interacting Lattice Gas Simulation, R.B.
Pandey and J.F. Gettrust, Physica A 358, 437 (2005).
o
Structural
response in steady-state flow of a multi-component driven system: Interacting
lattice gas simulation, R.B. Pandey and J.F. Gettrust, Physica A 345, 555 (2005).
o
Self-organized
phase segregation in a driven flow of dissimilar particles mixtures, R.B.
Pandey, J.F. Gettrust, R. Seyfarth, and L.A. Cueva-Parra, Int. J. Mod. Phys. C 14, 955 (2003).
7. Theoretical
immunology
Understanding the population dynamics of
cellular elements in immune response, particularly in HIV, is one of the most
difficult issues. We have developed models using cellular automata (CA),
stochastic CA, and
Related publications:
o
Effects
of viral mutation on cellular dynamics in a
o
Viral
load and stochastic mutation in a Monte Carlo simulation of HIV, H.J. Ruskin,
R.B. Pandey, and Y. Liu, Physica A 311,
213 (2002).
o
Effect
of mutation on helper T-cells and viral population: A computer simulation model
for HIV, R. Mannion, H. Ruskin, and R.B. Pandey, Theor. Biosci. 119, 10 (2000).
o
Effect
of cellular mobility on immune response, R.B. Pandey, R. Mannion, and H.
Ruskin, Physica A 283, 447 (2000).
8. Econophysics: Theoretical modeling of
stock fluctuations.
Related publications:
o
A
momentum trading approach to technical analysis of DOW Jones industrials, H.
Wang and R.B. Pandey,Physica A 331, 639 (2004).
o
Momentum
analysis of DJI stocks near sharp rise, crash, and consolidation, H. Wang and
R.B. Pandey, Physica A 334, 524 (2004).
o
Effect
of trading momentum and price resistance on stock market dynamics: a glauber
Monte Carlo simulation, F. Castiglione, R.B. Pandey, and D. Stauffer, Physica A
293, 223 (2001).
9. Critical phenomena: Thermal and geometrical phase transitions:
early efforts involve multi-critical phenomena in disordered magnetic systems
using renormalization methods. Percolation phase transitions involve computer
simulations.