Studies On Ion And Nucleotide Force Fields Used In Biomolecular Simulations.

Overview

Pair-potential models in molecular dynamics simulations are actively utilized in various fields and have been shown to accurately model and reveal a variety of phenomena occurring at the atomistic level. However, the models still have room for improvement. Changing parameters involved in the pair-potential can completely change the potential energy map of systems. Since there are too many degrees of freedom in the determination of the parameters, obtaining the most optimized parameters is almost impossible. For ...
See more details below
This Paperback is Not Available through BN.com
Sending request ...

More About This Book

Overview

Pair-potential models in molecular dynamics simulations are actively utilized in various fields and have been shown to accurately model and reveal a variety of phenomena occurring at the atomistic level. However, the models still have room for improvement. Changing parameters involved in the pair-potential can completely change the potential energy map of systems. Since there are too many degrees of freedom in the determination of the parameters, obtaining the most optimized parameters is almost impossible. For this reason, any pre-existing parameters can be challenged whenever new methods of optimization are discovered. In particular, the parameters for alkali and halide ions had an urgent need for revision due to serious artifacts, such as early precipitation below saturation concentration. We presumed that the problems were mainly caused by not considering ion-ion interactions in the parameterization. Lattice constants and lattice energy of alkali-halide salts were used to reparametrize in addition to hydration free energies. The revised ion parameters were tested and they were good at reproducing the new target properties as well as hydration free energies, which were traditionally regarded as important properties for the ions. Other various properties of the ions related to ion dynamics and energetics in aqueous solutions were measured and compared with those from old parameters and experimental results. Some properties showed qualitative agreements with experimental results but some did not. In parallel with the investigation on ion parameters, AMBER nucleotide force fields were tested. Recently, the AMBER nucleotide force field was revised because alpha/gamma dihedral angles of the backbone of polynucleotides were wrongly populated. To test the new force field called parmbsc0, we attempted to reveal coralyne-poly(dA) duplex structures utilizing both old and new force fields. We detected slight difference between them but overall, two force fields gave similar prediction. However, the readjustment of the new force field showed clear improvement in the population of the backbone torsions.
Read More Show Less

Product Details

  • ISBN-13: 9781244004115
  • Publisher: BiblioLabsII
  • Publication date: 9/11/2011
  • Pages: 124
  • Product dimensions: 7.44 (w) x 9.69 (h) x 0.26 (d)

Customer Reviews

Be the first to write a review
( 0 )
Rating Distribution

5 Star

(0)

4 Star

(0)

3 Star

(0)

2 Star

(0)

1 Star

(0)

Your Rating:

Your Name: Create a Pen Name or

Barnes & Noble.com Review Rules

Our reader reviews allow you to share your comments on titles you liked, or didn't, with others. By submitting an online review, you are representing to Barnes & Noble.com that all information contained in your review is original and accurate in all respects, and that the submission of such content by you and the posting of such content by Barnes & Noble.com does not and will not violate the rights of any third party. Please follow the rules below to help ensure that your review can be posted.

Reviews by Our Customers Under the Age of 13

We highly value and respect everyone's opinion concerning the titles we offer. However, we cannot allow persons under the age of 13 to have accounts at BN.com or to post customer reviews. Please see our Terms of Use for more details.

What to exclude from your review:

Please do not write about reviews, commentary, or information posted on the product page. If you see any errors in the information on the product page, please send us an email.

Reviews should not contain any of the following:

  • - HTML tags, profanity, obscenities, vulgarities, or comments that defame anyone
  • - Time-sensitive information such as tour dates, signings, lectures, etc.
  • - Single-word reviews. Other people will read your review to discover why you liked or didn't like the title. Be descriptive.
  • - Comments focusing on the author or that may ruin the ending for others
  • - Phone numbers, addresses, URLs
  • - Pricing and availability information or alternative ordering information
  • - Advertisements or commercial solicitation

Reminder:

  • - By submitting a review, you grant to Barnes & Noble.com and its sublicensees the royalty-free, perpetual, irrevocable right and license to use the review in accordance with the Barnes & Noble.com Terms of Use.
  • - Barnes & Noble.com reserves the right not to post any review -- particularly those that do not follow the terms and conditions of these Rules. Barnes & Noble.com also reserves the right to remove any review at any time without notice.
  • - See Terms of Use for other conditions and disclaimers.
Search for Products You'd Like to Recommend

Recommend other products that relate to your review. Just search for them below and share!

Create a Pen Name

Your Pen Name is your unique identity on BN.com. It will appear on the reviews you write and other website activities. Your Pen Name cannot be edited, changed or deleted once submitted.

 
Your Pen Name can be any combination of alphanumeric characters (plus - and _), and must be at least two characters long.

Continue Anonymously

    If you find inappropriate content, please report it to Barnes & Noble
    Why is this product inappropriate?
    Comments (optional)