Biophysics

The majority of graduates in the Biophysics program have been undergraduate majors in physics or physical chemistry, although others have come from areas such as biology and electrical engineering. Consequently, the course requirements for admission are somewhat elastic, with a focus on more quantitative areas. The degree program is designed to be completed in a maximum of six years. The program is highly flexible, and special effort has been devoted to minimizing formal requirements.

The first part of the program seeks to introduce the students directly to the faculty members and their research, enabling the student to make a considered choice of research advisor, and to involve the student in the diverse areas of biophysics through laboratory as well as course work. The first year's training in the Biophysics Program provides an introduction to five diverse areas of Biophysics:

1. Structural Molecular Biology
2. Cell and Membrane Biophysics
3. Molecular Genetics
4. Physical Biochemistry
5. Neuroscience

Biophysics, Introduction to Laboratory Research, brings professors from all over the University for one-hour seminars on their specific areas of research interest, allowing the students a period of time to familiarize themselves with research opportunities at their first laboratory rotation later in the first semester.

First Year:

Several rotations as well as course work are completed in the year to year-and-a-half of study. A year's work for a resident student normally consists of four courses (eight half-courses) of advanced grade.

Second Year:

Students continue with course work and laboratory rotations.

A semester of teaching is required in the second year.
Students chose their research advisor by the end of their second year.
Preliminary Qualifying examination must be completed by the end of the second year. Student must pass this exam before beginning thesis research.

Third Year and beyond:
Student meets at least annually with his or her Dissertation Advisory Committee (DAC).
Student engages in a period of intensive research culminating in publications and the receiving of the Ph.D. degree.

Areas of concentration and suggested course work is as follows:

* Structural Molecular Biology
o Genomics and Computational Biology
o Structure and Function of Proteins and Nucleic Acids
o Structural Biology of the Flow of Information in the Cell
o Crystal Symmetry, Diffraction, and Structure Analysis
o Chemical Biology
o Molecular Structure and Function
o Molecular Biology
o Proteins: Structure, Function and Catalysis
o Macromolecular NMR

* Molecular Genetics
o Molecular Genetics of Neural Development and Behavior
o Developmental Genetics and Genomics
o Molecular Mechanisms of Gene Control
o Principles of Genetics

* Physical Biochemistry
o Physical Chemistry
o Frontiers in Biophysics
o Molecular Biophysics and Biophysical Chemistry
o Topics in Biophysics
o Quantum Mechanics I
o Single-molecule Biophysics

* Cell and Membrane Biophysics
o Molecular and Cellular Immunology
o Biochemistry of Membranes
o Molecular Biology of the Cell
o Growth Factors and Signal Transduction

* Mathematical Biophysics
o Methods of Analysis and Applications
o Introduction to Systems Analysis with Physiological Applications
o Signals and Systems
o Nonlinear Dynamical Systems
o Population Genetics
o Population and Community Ecology
o Complex and Fourier Analysis
o Ordinary and Partial Differential Equations
o Mathematical Modeling
o Physical Mathematics I, II
o Fundamentals of Computational Biology
o Mathematics in Biology

* Neurosciences
o Systems Neuroscience
o Cellular Basis of Neuronal Function
o Experimental Neuroscience
o Molecular and Developmental Neurobiology
o Neural Signal Processing
o Introduction to Neurobiology
o Neurophysiology of Central Circuits
o Molecular Neurobiology

Biophysics is an interdisciplinary science that uses the methods of physical science to study biological systems.^[1] Studies included under the branches of biophysics span all levels of biological organization, from the molecular scale to whole organisms and ecosystems. Biophysical research shares significant overlap with biochemistry, nanotechnology, bioengineering, agrophysics and systems biology.

Molecular biophysics typically addresses biological questions that are similar to those in biochemistry and molecular biology, but the questions are approached quantitatively. Scientists in this field conduct research concerned with understanding the interactions between the various systems of a cell, including the interactions between DNA, RNA and protein biosynthesis, as well as how these interactions are regulated. A great variety of techniques are used to answer these questions.

Fluorescent imaging techniques, as well as electron microscopy, x-ray crystallography, NMR spectroscopy and atomic force microscopy (AFM) are often used to visualize structures of biological significance. Conformational change in structure can be measured using techniques such as dual polarisation interferometry and circular dichroism. Direct manipulation of molecules using optical tweezers or AFM can also be used to monitor biological events where forces and distances are at the nanoscale. Molecular biophysicists often consider complex biological events as systems of interacting units which can be understood through statistical mechanics, thermodynamics and chemical kinetics. By drawing knowledge and experimental techniques from a wide variety of disciplines, biophysicists are often able to directly observe, model or even manipulate the structures and interactions of individual molecules or complexes of molecules.

In addition to traditional (i.e. molecular and cellular) biophysical topics like structural biology or enzyme kinetics, modern biophysics encompasses an extraordinarily broad range of research, from bioelectronics to quantum biology involving both experimental and theoretical tools. It is becoming increasingly common for biophysicists to apply the models and experimental techniques derived from physics, as well as mathematics and statistics (see biomathematics), to larger systems such as tissues, organs, populations and ecosystems.

Focus as a subfield

Biophysics often does not have university-level departments of its own, but has presence as groups across departments within the fields of molecular biology, biochemistry, chemistry, computer science, mathematics, medicine, pharmacology, physiology, physics, and neuroscience. What follows is a list of examples of how each department applies its efforts toward the study of biophysics. This list is hardly all inclusive. Nor does each subject of study belong exclusively to any particular department. Each academic institution makes its own rules and there is much overlap between departments.

• Biology and molecular biology - Almost all forms of biophysics efforts are included in some biology department somewhere. To include some: gene regulation, single protein dynamics, bioenergetics, patch clamping, biomechanics.
• Structural biology - Ångstrom-resolution structures of proteins, nucleic acids, lipids, carbohydrates, and complexes thereof.
• Biochemistry and chemistry - biomolecular structure, siRNA, nucleic acid structure, structure-activity relationships.
• Computer science - Neural networks, biomolecular and drug databases.
• Computational chemistry - molecular dynamics simulation, molecular docking, quantum chemistry
• Bioinformatics - sequence alignment, structural alignment, protein structure prediction
• Mathematics - graph/network theory, population modeling, dynamical systems, phylogenetics.
• Medicine and neuroscience - tackling neural networks experimentally (brain slicing) as well as theoretically (computer models), membrane permitivity, gene therapy, understanding tumors.
• Pharmacology and physiology - channel biology, biomolecular interactions, cellular membranes, polyketides.
• Physics - biomolecular free energy, stochastic processes, covering dynamics.
• Quantum biophysics involves quantum information processing of coherent states, entanglement between coherent protons and transcriptase components, and replication of decohered isomers to yield time-dependent base substitutions. These studies imply applications in quantum computing.
• Agronomy and agriculture

Many biophysical techniques are unique to this field. Research efforts in biophysics are often initiated by scientists who were traditional physicists, chemists, and biologists by training.