498: Statistical Physics, Biological Information and Complexity

Homework 1 Essays: The Molecules of Life
 

Author: Anoush Aghajani-Talesh
Title: DNA Computer (41 kb)

Abstract:

This essay discusses the paper "Breaking DES Using a Molecular Computer" by Dan Boneh et. al., which describes an algorithm using DNA and standardized biotechnological procedures to break the Data Encryption Standard (DES).
Author: Tommy Angelini
Title: Amyloidosis (25 kb)

Abstract:

Experimental evidence has shown that many amyloid fibrils share similar structural characteristics, independent of the specific nature of their constituent proteins.  These experiments are presented and critiqued, and further experiments on amyloid fibrils are proposed.
Author: Marco V. Bayas
Title: Designability of lattice model heteropolymers (27 kb)

Abstract:

The aim of this article is to review a model for the calculation of the designability of proteins. According to the model, proteins which are stable
can tolerate mutations without a lost of activity and consequently without lost of structure. Of course this was known experimentally but there was not a
theoretical framework for its interpretation.
Author: Soon Yong, Chang
Title : Review of paper "A thermodynamic model for prebiotic RNA-protein co-evolution" by Erzan Tuzel and Ayse Erzan, cond-mat/0107315 v1 Jul/2001

Abstract:

In this study, the situation that precedes the existence of the cells (prebiotic) is supposed. At the same time, the RNA is allowed to have an independent existence from the DNA acting as the synthesizer of the protein. There is supposed to be a primeval "soup" rich in different amino acid molecules where the RNAs as well as the protein molecules float freely. The evolutionary advantages that favor those proteins (and RNAs that encode them) that can act as "heat pumps" folding and unfolding is studied.
Author : Swarbhanu Chatterjee.
Title  : Prebiotic RNA-Protein Coevolution and the origin of Life (75 kb)

Abstract :

It is believed by today's scientific community that before the DNA world, there was an RNA world in which the RNA replicated by themselves and RNA and protein coevolved. Authors Tuzel and Erzan have suggested a thermodynamic model for RNA-Protein coevolution in Pre-Cambrain Rocks. I have described the model. Also, in my opinion, the biological definition of life to be a cellular phenomenon should be extended to encompass life of other forms as well.
Author:Jordi Cohen
Title: The "LEGO" properties of DNA (615 kb)

Abstract:

This essay gives an overview of recent developments in DNA nanotechnology. DNA strands can be coded to self-assemble into complex macroscopic structures (such as polyhedra, knots and lattices). Methods for controlling the geometry, topology and rigidity of such structures are described.
Title: Charge transfer in DNA - Role of Structural Fluctuations (102 kb)
Author: Parag Ghosh

Abstract:

A mechanism of charge transport through DNA has been discussed. It has been proposed that charge transport in DNA is brought about by structural
fluctuations. Thermal fluctuations induce structural disorder which interferes with the Pi-orbital overlap and the corresponding tunneling frequency. This
results in longer relaxation times and a two-step decay process in high temperature strong coupling limit.
Author: Matt Gordon
TitleThe Future of Genomic Sequencing (63 kb)

Abstract:

The current methods of whole-genome DNA sequencing is reviewed, and the computational and physical limitations of these methods are discussed.  Then, three new methods for sequencing currently under development are presented: DNA microchannels, single molecule fluoresence, and atomic force microscopy.  These techniques are analyzed for their suitability for whole genome sequencing, and their pros and cons are discussed.
Author:Paul Grayson
Title: Pulling apart DNA and RNA (59 kb)

Abstract:

Measurements of individual molecules, especially DNA and RNA, are necessary for an understanding of many biological processes.  This essay describes several recent experiments that have begun to measure the forces holding DNA and RNA together - by pulling them apart.
Author: Chalermpol Kanchanawarin
Title: Symmetry in Protein Structures (697 kb)

Abstract:

With many protein structures (now over 16,000 proteins) solved and a lot of experiments done over the past decade, it has been found that most of
the proteins form symmetrical oligomeric complexes consisting of two or more identical subunits. Symmetry seems to be a very important ingredient in
understanding protein structures and functions.
Author: David Larson
Title: Twisting and Writhing Numbers in Circular DNA (70 kb)

Abstract:

This paper discusses the twisting and writhing numbers of circular DNA.  It defines the numbers and attempts to explain what they mean and how they can further current understanding of DNA behavior.
Author:      Yan Li
Title:      Uncoiling DNA-- Single Molecule experiment of relaxation of DNA by a type II topoisomerase (192kb)

Abstract:

This article reviewed T.R.Strick's experimental results of type II topoisomerases of Drosophia melangogaster on a substrate of a linear, linked
DNA molecule.Their results not only yielded important information on the efficiency and affecting factors of the enzyme function rate, but also
presented a well-controlled, reversible way to carry out investigations into single molecules.
Author: Ian O'Dwyer
Title: Elucidation  of RNA secondary structures using genetic algorithms (77kb)

Abstract:

Author: Rahul Roy
Title: Micromechanics of RNA Polymerase (69 kb)

Abstract:

The molecular mechanism by which the RNAP moves along the DNA template, synthesizing a RNA chain by converting the free energy of the nucleotide binding and hydrolysis into a force directed along the DNA axis has been an interesting and hot topic both experimental and theoretical research. In this work, the energetics based model developed by George Oster and co-workers is reviewed and an experimental set up to test the reported step size d of the RNAP motion along the DNA, is proposed.
Author: Prasanth Sankar
Title: Motor Proteins (813 kb)

Abstract:
 

This essay describes the biological and physical approaches used to study the motor proteins of Kinesin family. Structural studies and structural changes during the ATP cycle dominates the biological description of these interesting proteins where as physical description of motion of these proteins uses a Brownian ratchet mechanism
Author:    Martin Ph. Stehno
Title:       Molecular Computers - Computing with DNA (28kb)

Abstact:

Molecular computers (MCs) are thought to be devices for massive parallel computing. Possible ways of coding the computational problems as well as the neccessary "DNA operations" have been worked out already, and - on a small scale - computations were carried out successfully. Handling the errors of molecular computations is of special interest and will be discussed in detail. Here also lie the pitfalls whem upscaling existing MC architectures to computational problems of larger size.
Author: Kapil Rajaraman
Title: The quantum basis for genetic information processing (134 kb)

Abstract:

There have been a number of hypotheses put forward to explain the number of nucleotides (4) and the number of amino acids (20). In this essay, we
discuss an explanation given on the basis of quantum computing and Grover's algorithm. The essay also describes the proposed method of
DNA replication.
Author: Elizabeth Villa Rodriguez
Title: Ribosome rocks (853 kb)

Abstract:

This essay reviews the current reaseatch on the ribosome, and makes a proposition on how physicists could contribute to the understanding of this
fascinating complex system.
Author: Kalin Vestigan
Title: Simplification of Topology by Type II Topoisomerases and Kinetic Proofreading model (161 kb)

Abstract:

People study topoisomerases from many di erent perspectives: protein structure, detailed atomic level mechanisms of how they work, single molecular experi- ments, e ects of mutations on enzyme function, etc. However, the  rst question I have as a beginner is what topoisomerases do. I would also like to imagine at least one physically plausible mechanism capable to account for the observed functions. I will discuss a relatively recent experimental paper by Rybenkov et. al.(1997), revealing unexpected abilities of various type II topoisomerases, and theoretical papers by Yan, et al.  giving a possible explanation.
Author: Qing-jun Wang
Title: How Do Physicists and Biologists Unravel the Mystery of Genetic
Code? (7.9 Mb)

Abstract:

This essay describes and comments how physicists and biologists unravel the mystery of genetic code. Physicists started out to study the genetic
code by looking for empirical relations between chemical compositions of RNA molecules and amino acids. They get to pursue the fundamental reasons
why the genetic code is just the way by studying the degeneracy and symmetry breaking of genetic code. For biologists, genetic code is a
"periodic table of elements for biology". They are focus on studying the large amount of genetic code variants and the evolution of genetic code.
Author: Paul Welander
Title:  A Thermodynamic Model for Prebiotic RNA-Protein Co-evolution (101 kb)

Abstract:

In a recent paper, Erkan Tuzel and Ayse Erzan explore a thermodynamic model for the selection and evolution of proteins and RNA molecules in the
pre-biotic world. The folding and unfolding of the protein molecules is treated as a heat pump whose efficiency depends on the entropy gap between
states and the folding rate. Those proteins that are most efficient, along with the RNA that encoded them, are then favored in the evolutionary
process. This method, the authors believe, is partly responsible for the selection of proteins observed today.
Author:  Jian Xu
Title: Single Molecule Experiments of RNA polymerase in DNA Transcription (1.3 MB)

Abstract:

This essay describes some single molecule experiments of RNA polymerase in DNA transcription.  Different experimental schemes are explained, advantages and shorting comings are also addressed.  And I also designed a experimental setup that can measure the force, translocation rate, and the rotation rate
simultaneously.
Author: Jin Yu
Title: A simple review of multifractal analysis of complete  genomes  (1.8 Mb)

Abstract:

This essay introduces the analysis of complete genome by multifactal method, which provides a simple yet powerful method to amplify the difference between a DNA sequence(coding or noncoding) and a random sequence as well as to distinguish DNA sequences themselves in more details.
Author:     Guojun Zhu
Title:      Chaperon in Protein Synthesize (76 kb)

Abstract:

This essay describes how the chaperon help protein folded into the active structure in the ribosome.

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