You can also look and see how much free space your database has and how often the database is extending the database. If the extend size is too large, this can cause database queries to timeout. With the database file being only 3.5 GB this probably isn't all that likely unless the disk drives are too overloaded. You can check to see if the disk drives are being overloaded by using performance monitor and checking the disk queue, reads per second and writes per second.
Dig Deeper on Microsoft SQL Server Performance Monitoring and Tuning
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