Fill in the gaps with appropriate forms of the words in brackets

1. In statistics, frequency is defined as the proportion of individuals falling within a certain category in relation to the total number of individuals under ______________(consider).

2. In general, the ______________(extend) to which gene flow can hinder the effects of natural selection should depend on the relative strengths of the two processes.

3. To confirm the ______________(involve) of microtubules as sensors of directional force in cell elongation, some protoplasts were incubated prior to centrifugation with a chemical herbicide, APM, which disrupts microtubules.

4. Species with little genetic ______________(vary) are generally at significantly greater risk of extinction than more ______________(vary) species, simply because they have a more limited arsenal with which to respond to the vagaries of environmental change.

5. The complex differentiation that we associate with advanced life-forms ______________(depend) on multicellularity and sexuality, which must have been highly advantageous to have evolved ______________(depend) so often.

6. The cells tend to hang together in chains, a feature that calls to mind the ______________(derive) of single-celled yeasts from multicellular ancestors.

Translate into Russian

1. It is in muscle only that, owing to the mechanical nature of its function, we find the particles of the contractile structure arranged in such an orderly fashion which allows us to separate them easily.

2. Judging by their appearance we would expect the muscles to have a uniformly positive DR.

3. We have shown that muscle does contain a negatively doubly refracting substance which is about 20% of the total protein.

4. What the meaning and importance of this protein is we do not know.

5. Why this protein has a periodic distribution we do not know.

6. That the periodicity of the N-protein is rather the result of motion of muscle than its cause is supported by the fact that cells in cultures of embryonic heart muscle contract first and develop cross-striation after.

7. He found that the faster the muscle, the narrower its segmentation.

8. If at rest, muscle is soft and plastic; and if it were not so, we could not be able to move at all.

9. Contracting muscle is stiff and hard as it has to be if it has to do work.

10. In relaxation we would expect the muscle to become almost fluid to contain globules instead of threads, the mobility of which facilitates rearrangement into the resting structure without much inner friction.

11. This failure to explain biological phenomena in terms of classical chemistry suggests that there is something wrong with our basic conceptions of structure of living matter, and in order to understand structure and its biological function we have to look for a new theory of the solid state which allows us to look upon a greater number of molecules as units.

12. We have to apply this theory to living structure and see whether it leads us any further in the understanding of biological phenomena.

13. There is no reason to reject this theory provided that the particles possess two basic qualities.

14. In the polypeptide chain of proteins for every CO there is one NH per amino-acid, the repeating unit of the back-bone being NH-C-CO.

15. In earlier studies the single H-bridges have been dealt with as individual units. The bond electrons in the NH and CO were looked upon as localized, the II with its electron only being shared to some extent by the N and the CO, giving a low resonance energy of about 6000 cal.

16. The deeper knowledge of this mechanism can be expected to answer one of the greatest mysteries of biology: the function of the nucleic material.

UNIT 23 Potential Energy Contour Tracing

Insofar as one is using a realistic analytical function to represent the interatomic and/or inter-molecular potential, a molecular dynamics simulation can be regarded as a reliable facsimile of the actual situation. One can also place considerable trust in the observed dynamical behaviour of the system being investigated. There is, nevertheless, a severe disadvantage, namely that of the brevity of the overall simulation. As was noted in the previous section, the optimal time step in molecular dynamics is typically about 10^-14 s, so even a simulation spanning 10⁶ time steps would cover only 10^-8 s of real time, despite the fact that it would consume several hours on a 2001-vintage computer; and 10^-8 s is only about a millionth of the time it takes a typical protein to fold into its operational conformation.

It is frequently the case that one is not so much interested in following the actual dynamics as in predicting the minimum-energy conformation of a large molecule such as a protein. This is not yet possible, at the time this book is being written, but some progress can be made in charting the energy landscape in the high dimensionality required to adequately describe a molecule comprising many atoms. The point here is that each atom's position requires specification of three Cartesian coordinates, so a complete description of a molecule comprising N atoms requires one to take account of 3N coordinates. And because the potential energy is influenced by the position of each and every atom, finding the lowest-energy configuration of the molecule involves investigation of a potential-energy surface (or manifold) in 3N dimensions.

A molecular dynamics simulation does probe this potential-energy surface, of course, but it does so by exploring the energy barriers between local minima, in the haphazard fashion that characterizes thermal motions. The purpose of potential energy contour tracing (PECT), on the other hand, is to probe the topology of the energy manifold in a manner that is inaccessible to the thermal regime. A method is available which enables the state point to run around contours of constant potential energy, thus giving an indication of the local topology of the energy manifold. A simple analogy of these contours is seen in a geographical map, which depicts the contours of equal height above sea level.

Define the following words using a dictionary

Facsimile, simulation, severe, brevity, dimensionality, manifold, to chart

Complete the sentences

1. One can also place considerable trust in…
2. It is frequently the case that…
3. Some progress can be made in...
4. The point here is that each atom's position requires…
5. Because the potential energy is influenced by the position of each and every atom,…
6. A molecular dynamics simulation does probe this potential-energy surface, of course,...
7. The purpose of potential energy contour tracing (PECT), on the other hand, is…
8. A method is available which…