The following is a synopsis of major published papers by Eshel Faraggi.

**Protein Sequence/Structure/Function:**

Dihedral Angles, Secondary Structure, Accessible Surface Area, and Contact Maps :

** Eshel Faraggi, Yuedong Yang, Shesheng Zhang, and Yaoqi Zhou, "Predicting Continuous Local Structure and the Effect of Its Substitution for Secondary Structure in Fragment-Free Protein Structure Prediction". Structure 17, 1515-27 (2009)*

* Eshel Faraggi, Bin Xue, and Yaoqi Zhou, "Improving the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins by guided-learning through a two-layer neural network". Proteins 74, 857-71 (2009)

* Bin Xue, Ofer Dor, Eshel Faraggi, and Yaoqi Zhou, "Real-value prediction of backbone torsion angles". Proteins 72, 427-33 (2008)

* Bin Xue, Eshel Faraggi, and Yaoqi Zhou, "Predicting residue-residue contact maps by a two-layer, integrated neural-network method".Proteins 76, 176-83 (2009)

** Yaoqi Zhou, and Eshel Faraggi, "Prediction of one-dimensional structural properties of proteins by integrated neural network". Protein Structure Prediction: Method and Algorithms , edited by H. Rangwala and G. Karypis, Wiley, (2010)*

The relationship between the amino acid sequence of a protein, its structure and its function are one of the grand-challenges of twenty-first century science. In the first phase of tackling this big question we have been focused on the prediction of so called one-dimensional structure features. These include properties such as the protein secondary structure, its backbone dihedral angels, its accessible surface area, and contact numbers. Contact maps are an extension of contact numbers to two dimensions where one is interested in the distance matrix between the residues of the protein. The aim of this endeavor is to eventually use these structure features to constrain predictors of tertiary (three-dimensional) protein structure. Combining several approaches, among them development of a guided neural network and proper use of the bimodal distribution of the dihedral angles we were able to significantly improve the predictions of all these features, approaching for the first time the accuracy of nuclear magnetic resonance based assignment of dihedral angles. Our work further showed that using predicted dihedral angles as constraints results in an improvement of 100% in tertiary structure prediction as compared to using secondary structures.

Tertiary Structure Prediction:

* *Y. Zhou, D. Yuan, Y. Yang, E. Faraggi, H. Lei, "Trends in template/fragment-free protein structure prediction". (Invited feature article) Theor. Chem. Accounts, in press (2010).*

The overall goal of protein structure prediction is to predict the three dimensional structure of a protein given its amino acid sequence. Currently a new version of the SPARKS server for tertiary structure prediction is being developed. The family of SPARKS servers are highly regarded in the field and have been among the top performers in recent Critical Assessment of Protein Structure Prediction (CASP) competitions. The new generation of the SPARKS server will be built on top of the SPINE-X server, using its predictions as constraints on template alignments and as initial values/constraints for ab-initio predictions.

Dihedral Angle Fluctuations and Protein Disorder:

* *Tuo Zhang, Eshel Faraggi, and Yaoqi Zhou, "Fluctuations of backbone torsion angles obtained from NMR-determined structures and their prediction". Proteins, in press (2010).*

A problem intimately related to the structure of a protein is the amount of intrinsic disorder it posses. That is, given a folded protein how much of it doesn't have a well-defined constant structure. By working with proteins whose structure was resolved by NMR we were able to design the first predictor for the amount of fluctuations of the resolved dihedral angles and tie this to the amount of disorder in the protein. Disordered proteins are a very hot topic in proteomics due to their fundamental and practical applications.

**Dynamics
of Ferromagnetism:**

Ferromagnetism, Hysteresis and Chaos:

* *Daniel T. Robb, Linda E. Reichl,
and Eshel Faraggi, "Simulation of hysteresis in magnetic
nanoparticles with Nose thermostatting". Physical Review E
67(5), 056130 (2003).*

Much of the dynamics of ferromagnetism has to do with the temperature it is at. One method of modeling temperature is essentially assuming that the system is coupled to a thermostat. In this paper this highly analytical method was utilized while showing the emergence of chaos in the local magnetization of a growing ferromagnet. This study has significant impact on the proper use of a major model of ferromagnetism. The use of this method allowed the modeling of nanoscale hysteresis curves.

The Dilute Ferromagnet:

* *Eshel Faraggi, Linda E. Reichl,
and Daniel T. Robb, "Magnetic behavior of partially filled
finite Ising surfaces". Physical Review B 74(1) 014407 (2006).*

A major question facing any use of magnetic materials is the minimum usable ferromagnetic density. A calculation based on the methods of statistical mechanics, and first performed in the reference above demonstrated that local ferromagnetic order exists bellow the previously accepted minimum value, known as the percolation threshold. This local phase of magnetization, known as superparamagnetism, will determine the ultimate storage capacity of magnetic storage devices such as hard-drives and holds one of the keys to spintronic applications.

Hysteresis:

* *Eshel Faraggi, Linda E. Reichl,
and Daniel T. Robb, "Magnetic behavior of partially filled
finite Ising surfaces". Physical Review B 74(1) 014407 (2006).*

* *Corneliu Nistor, Eshel Faraggi,
J. L. Erskine, "Magnetic Energy Loss in Permalloy Thin Films and
Microstructures". Physical Review B 72, 014404 (2005). *

* *Eshel Faraggi, "Explicit
solutions to phenomenological models of magnetization reversal of
thin ferromagnetic films in the presence of a sawtooth magnetic
field". Journal of Magnetism and Magnetic Materials 303(1), 49
(2006).*

Hysteresis is the fundamental building block behind magnetic memory. The processes of storing and retrieving information requires energy that is converted into heat (dissipation). A very important question regarding hysteresis is the dependence (or scaling) of this dissipation of the system parameters. Most notably on the frequency of the sweeping field since this will determine the speeds at which writing is possible. In the references above it was shown that the dependence on frequency changes as the temperature and structure of the ferromagnet are changed, and a phenomenological model of hysteresis was developed and solved. This model was able to analytically predict hysteresis losses for over nine decades of frequency (nine orders of magnitude). With the aid of this phenomenological model it was also possible to illuminate more on the breakdown of the so called adiabatic scaling.

Locally Converging Algorithms:

* *Eshel Faraggi and Daniel T. Robb,
"Locally converging algorithms in Ising models". Physical Review B 78(13) 134416 (2008).*

An offshoot from the investigation into the dilute ferromagnet is the development of the locally converging algorithm for the critical temperature. This algorithm is a continuation of the ideas of the invaded cluster algorithm which was developed in the 1990's. These models contain feedback loops that drive the system towards their critical points automatically. The full impact of these models is not well understood at this time, but their impact will range from a better understanding of the critical point of ferromagnetism to self-adapting algorithms for complex systems.

**Spherical
Absorber:**

A ball immersed in fluid and illuminated by a laser pulse allows fundamental observations throughout the realm on condensed matter. My research focuses on these absorbers as models for melanosome that are present in our skin, and most notably in our eyes where they serve, among other functions, to shield the bloodstream from radiation. The sizes of the absorbers I model range from tens of nanometers to several microns, while melanosomes are approximately one micrometer in diameter.

Shockwaves:

* *Eshel Faraggi, Bernard S.
Gerstman, and Jinming Sun, "Biophysical Effects of Pulsed Lasers
in the Retina and Other Tissues with Strongly Absorbing Particles:
Shockwaves and Explosive Bubble Generation". Journal of
Biomedical Optics 10, 64029 1-12 (2005).*

** Bernard S. Gerstman, Shijun Wang,
and Eshel Faraggi, "Ab-Initio Calculations for Shock Wave and
Bubble Production with Gaussian Temporal Laser Pulses".
Proceedings of the SPIE, Progress in Biomedical Optics and Imaging,
Vol. 5319, pp. 217-223 (2004)*

** Eshel Faraggi, Shijun Wang, and
Bernard Gerstman, "Stress confinement, shock wave formation, and
laser-induced damage". Proceedings of the SPIE Vol. 5695, pp.
209-215 (2005).*

* *Eshel Faraggi, Bernard S.
Gerstman, and Shijun Wang, " Linear approximation for shock wave
production by the spherical absorber". (2006).*

One of the multitude of phenomena occurring in the illuminated spherical absorber is a shockwave. This wave, emitted for ultrashort pulses (sub nanosecond), are important for a variety of applications, e.g., underwater explosive detonation. In the context of melanosomes these shockwaves can be most damaging to the surrounding biological tissue. In a first of a kind calculation, the shockwaves produced by the melanosome were studied as a function of the laser/medium characteristics, as well as their decay in the media. Linear approximations were carried out to produce robust, simple, analytical expressions for the magnitude of the shockwaves as a function of the system parameters.

Bubbles:

* *Eshel Faraggi, Bernard S.
Gerstman, and Jinming Sun, "Biophysical Effects of Pulsed Lasers
in the Retina and Other Tissues with Strongly Absorbing Particles:
Shockwaves and Explosive Bubble Generation". Journal of
Biomedical Optics 10, 64029 (2005).*

** Bernard S. Gerstman, Shijun Wang,
and Eshel Faraggi, "Ab-Initio Calculations for Shock Wave and
Bubble Production with Gaussian Temporal Laser Pulses".
Proceedings of the SPIE, Progress in Biomedical Optics and Imaging,
Vol. 5319, pp. 217-223 (2004).*

Another very important aspect of the illuminated spherical absorber is the production of explosive vaporization around the melanosomes. These bubbles can be damaging to tissue, but they can also be used to stimulate repair in cells. One known mechanism for this is shock-protein generation. With the use of a custom designed simulation, the bubble production around melanosomes was studied. Besides giving researchers analytical predictions for the size of bubbles produced for a given laser, these results indicate the theoretical possibility of determining minimal bubble production in vivo. This is of vital importance for several laser surgery applications that require minimum bubble production. Such studies may eventually offer a cure for some forms of blindness.

Resonant Absorption:

* *Eshel Faraggi, Bernard S.
Gerstman, "Resonant absorption of pulsed laser radiation by a
spherical absorber". J. Appl. Phys. 102(12), 123505 (2007).*.

* *Eshel Faraggi, Bernard S.
Gerstman, and Shijun Wang, "Response to pulsed radiation by a
spherical solid absorber immersed in a transparent fluid".
Proceedings of the SPIE Vol. 5696, pp. 101-109 (2005).*

* *Eshel Faraggi, Bernard S.
Gerstman, "Resonant absorption in nanometer gold spherical
particles". Proceedings of the SPIE, Vol. 6084, (2006).*

A spherical absorber acted upon by consecutive laser pulses will behave differently depending on the duration between the pulses. For specific, resonant durations, the response has a highly acoustic component for example as shockwaves. For other durations the acoustic response is suppressed. Yet simple, this profound discovery presented in reference 8 implies that the interaction between lasers and matter can be manipulated by designing specific pulse sequences. Such considerations can greatly increase the potential of many laser applications. Most notably, in photo-dynamic therapy application for cancer.

Chaos:

* *Eshel Faraggi, Bernard S.
Gerstman, and Jinming Sun, "The emergence of nonlinear behavior
and chaos in laser irradiated spherical absorber". Chaos 17(1), 013101 (2007).*

** Bernard S. Gerstman, Eshel
Faraggi, and Jinming Sun, "Chaos in the pressure generated by
laser absorption by microparticles". Proceedings of the SPIE,
Vol. 6084, (2006).*

The existence of chaos in medical applications is intriguing. It presents both beneficial and hazardous prospects depending on the circumstances. In this set of publications the existence of chaos and its location in the parameter space of the spherical absorber system was established. These chaotic signals have a spiky nature and these unpredictable spikes tend to have large gradients which can cause damage. Of course anything that can cause damage can be made beneficial in various treatments, e.g., for killing cancer.

Superposition:

* *Eshel Faraggi, " A superposition test for the emergence of
nonlinearities in a laser irradiated spherical absorber".
Submitted to Physical Review Letters.*

The principal of superposition lays at the foundation of linear physics. In this forthcoming paper, the validity of superposition is tested and linked to the existence of nonlinear phenomena. Analytical expressions are proposed for the dividing line between the linear and nonlinear regimes of the system in parameter space.

Pulse Shape Dependence:

* *Eshel Faraggi, Bernard S.
Gerstman, and Shijun Wang, "Effect of temporal pulse shape in
laser absorption by a spherical absorber". Submitted to
the Journal of Lasers in Surgery and Medicine.*

The dependence of the thermomechanical response of a spherical particle on the temporal shape of the laser pulse is of interest to researchers wishing to utilize this system in various applications. In the above mentioned paper this dependence was studied. It was found that the most critical dependence of the response is for time scales that are longer than the critical acoustic time of the absorber.

**Biological
Cell Division:**

* *Eshel Faraggi, "The effects of symmetry on the dividing biological cell". Submitted to the Physical Review.*

* *Eshel Faraggi, "An
electrostatic model for biological cell division". http://arxiv.org/abs/1006.3961 (2006).*

A fundamental process associated with cellular biology is the division of a parent cell into two (or more) daughter cells. This process is common to almost all biological system and a better understanding of it will have profound implications for biology in general and medicine in particular. In this, first paper on this subject, a theoretical framework is developed for cell division where the mechanics of separation are carried out by electromagnetic interactions. If indeed cell division is governed by electromagnetism, this knowledge will help guide applications interacting with biological materials via electromagnetic interactions and will benefit medicine immensely.

**Discrete Time and Chaos:**

* *Eshel Faraggi, "Nonlinear behavior in Ferromagnetism: Simple observations and possible implications". http://arxiv.org/abs/nlin.SI/0209006 (2002).*

In this fun paper the Ginzburg-Landau model for ferromagnetism is analyzed for a simple system. Since for this system both a numerical and an analytical solution exist they can be analyzed concurrently. This analysis shows that for this system chaotic observations arise out of the discretization of time. That is, for continuous time, or if time steps are small enough as compared to a system dependent time scale no chaos will be observed. However, if transitions in time are discrete, with long enough steps, chaotic dynamics will be observed. Possible implications for giant ferromagnetic systems such as neutron stars are discussed.