Physics provides the fundamental theories for understanding biomolecules. For example, statistical mechanics, a cornerstone of modern physics, is also the foundation for understanding the behaviors of biomolecular systems. Electron transfer within protein matrices, which drives respiration and photosynthesis, can only be understood with the help of quantum mechanics.
In essence, an electron can hop from one position to another within a protein matrix only when the energy levels before and after the hop are equal. Importantly, many of the powerful tools for investigating biomolecules were initiated by physicists. X-ray crystallography provides a telling example. The subsequent mathematical formulation of the diffraction pattern by the Braggs, father and son Nobel Prize in Physics , ushered in the new field of X-ray crystallography. Similar paths can be traced for nuclear magnetic resonance spectroscopy , , and Nobel Prizes in Physics; and Nobel Prizes in Chemistry; and Nobel Prize in Physiology or Medicine , atomic force microscopy Nobel Prize in Physics , electron microscopy Nobel Prize in Physics , and single-molecule techniques such as optical tweezers Nobel Prize in Physics.
Many computational techniques - for example, molecular dynamics simulation - that are now widely used for modeling biomolecular systems also have their origins in physics.
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As Crick learned, you have to adjust from the "'elegance and deep simplicity"' of physics to the "'elaborate chemical mechanisms that natural selection has evolved over billions of years. The transition can be eased by collaborating with another biophysicist or a biologist.
However, despite the significant barrier to the transition from physics to biology, intellectually it is probably still far easier than the transition in the opposite direction! An important contribution of biophysicists to modern biology is the perspective that biological processes can be understood from the interactions between and within the constituent molecules. Therefore, the behaviors of biological systems can be predicted from physical principles. A biological problem that has been mostly tackled by biophysicists is protein folding, by which a nascent polypeptide chain coming off the ribosome finds its unique structure in its native environment.
The broad outlines of how the protein avoids the vast number of alternative conformations and quickly finds its native structure are now clear. Some may go as far as claiming the problem is solved. Biophysicists are now using very similar approaches to study the binding of proteins and other biomolecules as well as more complex biological processes. Biophysicists are largely responsible for dramatic increases in the spatial resolution of structural characterization and the temporal resolution of dynamical characterization, and for bringing the study of biological processes to the single-molecule level.
Biophysicists have demonstrated that many essential features of complex biological systems can be emulated by relatively simple computational models. In particular, artificial neural networks are shown to produce associative memory, an essential function of the brain.
Book Series: Methods in Experimental Physics
How the modeling work is labeled is less important than the fact that it is able to demonstrate that many essential biological features seem generic and robust. That is, they emerge from relatively simple models and are insensitive to details of the models. There are now similar efforts dealing with signaling and gene regulatory networks.
Still, a fundamental understanding of these processes will require considering the physical interactions between the molecules involved. One example is the theory of complex systems, in which a key concept is emergent properties. These are properties that are not intrinsic to the individual components of a system but are only produced when the components work together as a whole system. For instance, a neural network can produce memory only through the interactions of all the neurons in the network.
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In addition, biological problems have stimulated renewed interest in areas like stochastic processes and open, driven systems. Many biophysical concepts, theories, and tools were originally developed in physical chemistry. Binding affinity, key to characterizing specificity and selectivity in molecular interactions, derives from equilibrium constants of chemical reactions.
Rate theories and the stopped-flow technique for measuring rate constants are other examples.
A composite of processes addressed by biophysics. The depicted processes include the binding of the large and small subunits of the ribosome, the folding of a nascent protein, its binding to another protein, and its aggregation. The equilibrium constants and rate constants of these processes can be computed according to basic theories of physical chemistry, and can be changed by many orders of magnitudes by the structures, dynamics, and interactions of the constituent molecules.
It should also be recognized that these biophysical properties in the crowded native environment can differ significantly from those determined under dilute conditions of typical in vitro experiments Zhou et al. Many biophysicists have focused on biology at the molecular level, but more and more of them are now studying processes at the cellular level.
For example, the National Cancer Institute has funded 12 Physical Sciences-Oncology Centers, where physicists and cancer biologists are teamed up to uncover the physical principles that govern the emergence of cancer and its behavior at different scales. Tackling the challenging biological problems of the future will require ever closer integration of biology and physics in advancing new concepts and new experimental techniques.
A life scientist with a solid training in physics will have unique strengths in this integration. Research at the intersection of the physical and life sciences is full of opportunities. The blurring of the disciplinary boundary is a good sign! That said, at present most people doing biological research have been trained in traditional departments. As a result, there are still cultural differences. For example, a biochemist may be interested in reducing a complex biological process such as protein synthesis into a sequence of binding events and chemical reactions, whereas a biophysicist may be interested in the rate constants of these events.
So the biochemist identifies the constituent molecules and frames the biologically interesting questions, and the biophysicist then asks how do I explain the biochemical observations based on the structures and the interactions of the constituent molecules? Both are needed to discover how the biological process actually works. One clear trend is that biology is becoming more and more quantitative. Aggregation and self-assembly. The biomacromolecules. Viscoelasticity and bioreology. Phase transitions, glass transition and processes involved in cryopreservation protocols.
Elements of wave optics and quantum mechanics to understand the experimental methods of molecular biophysics, such as protein crystallography, photocorrelation spectroscopy and Brillouin spectroscopy, spectroscopic imaging techniques, STM and AFM microscopy. Reference texts Lecture notes, articles and chapters of textbooks suggested therein. Educational objectives The main objective of the course is to provide students with the basic knowledge to understand the theoretical fundamentals and some experimental methods of molecular biophysics, also in view of their application in cryopreservation.
The main knowledge gained will cover: - Constituents of matter and their biological interactions. Phase transitions and glass transition. Prerequisites Baisc Chemistry, Physics and Molecular Biology Teaching methods Face-to-face lessons on all topics covered by the course and laboratory experiments regarding photocorrelation spectroscopy, Brillouin, and Raman spectroscopic imaging. Other information Learning verification modality The exam consists in the presentation of individual seminars by students on topics regarding to the course, and an oral exam.
The oral exam in a discussion lasting about 30 minutes aimed at ascertaining the level of knowledge on technical content and methodology of the course the constituents of matter and their biological interactions. Phase trasitions and glass transition. Principles and potential of some experimental methods of molecular biophysics, such as protein crystallography, photocorrelation spectroscopy and Brillouin spectroscopy, spectroscopic imaging techniques, STM and AFM microscopy. Cryopreservation of cells and tissues: overall regulatory framework, national and international.
The problem of cryopreservation: chemical and physical aspects. Chemical-physical investigation techniques. The oral exam will also test the student communication skills and his autonomy in the organization and exposure of the theoretical topics. Extended program Elements of biological soft matter physics. Constituents of biological matter and their interactions.
Elements of wave optics. Electromagnetic waves. Interference, and diffraction. Bragg's law. Experimental methods: Protein crystallography. Photocorrelation spectroscopy and Brillouin spectroscopy.
Vibrational spectroscopies and their biophysical applications. Details Last update.